@article{butler_in_2001, title = {In Situ Synthesis of Oligonucleotide Arrays by Using Surface Tension}, volume = {123}, url = {http://dx.doi.org/10.1021/ja003758r}, doi = {10.1021/ja003758r}, abstract = {This work describes the in situ synthesis of oligonucleotide arrays on glass surfaces. These arrays are composed of features defined and separated by differential surface tension (surface tension arrays). Specifically, photolithographic methods were used to create a series of spatially addressable, circular features containing an amino-terminated organosilane coupled to the glass through a siloxane linkage. Each feature is bounded by a perfluorosilanated surface. The differences in surface energies between the features and surrounding zones allow for chemical reactions to be readily localized within a defined site. The aminosilanation process was analyzed using contact angle, X-ray photoelectron spectroscopy {(XPS),} and time-of-flight/secondary ion mass spectroscopy {(TOF-SIMS).} The efficiency of phosphoramidite-based oligonucleotide synthesis on these surface tension arrays was measured by two methods. One method, termed step-yields-by-hybridization, indicates an average synthesis efficiency for all four {(A,G,C,T)} bases of 99.9 +- 1.1\%. Step yields measured for the individual amidite bases showed efficiencies of 98.8\% {(dT),} 98.0\% {(dA),} 97.0\% {(dC),} and 97.6\% {(dG).} The second method for determining the amidite coupling efficiencies was by capillary electrophoresis {(CE)} analysis. Homopolymers of {dT} (40- and 60mer), {dA} (40mer), and {dC} (40mer) were synthesized on an {NH4OH} labile linkage. After cleavage, the products were analyzed by {CE.} Synthesis efficiencies were calculated by comparison of the full-length product peak with the failure peaks. The calculated coupling efficiencies were 98.8\% {(dT),} 96.8\% {(dA),} and 96.7\% {(dC).}}, number = {37}, journal = {Journal of the American Chemical Society}, author = {John H. Butler and Maureen Cronin and Keith M. Anderson and Giles M. Biddison and Francois Chatelain and Michael Cummer and Deborah J. Davi and Lawson Fisher and Albrecht W. Frauendorf and Felix W. Frueh and Carmen Gjerstad and Theresa F. Harper and Stephanie D. Kernahan and Danny Q. Long and Mylan Pho and John A. Walker and Thomas M. Brennan}, year = {2001}, pages = {8887--8894} }, @misc{_ink-jet-printable_????, title = {Ink-jet-printable phosphorescent organic light-emitting-diode devices}, url = {http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normal&id=JSIDE8000016000012001229000001&idtype=cvips&gifs=yes} }, @article{weaver_recent_2006, title = {Recent advances in phosphorescent {OLEDs} for small-and large-area-display sizes}, volume = {14}, journal = {Journal of the Society for Information Display}, author = {M. S. Weaver and R. C. Kwong and V. A. Adamovich and M. Hack and J. J. Brown}, year = {2006}, pages = {449} }, @article{chalmeau_self-aligned_2008, title = {Self-aligned patterns of multiple biomolecules printed in one step}, volume = {93}, url = {http://link.aip.org/link/?APL/93/133901/1}, doi = {10.1063/1.2990045}, number = {13}, journal = {Applied Physics Letters}, author = {J. Chalmeau and C. Thibault and F. Carcenac and C. Vieu}, year = {2008}, keywords = {atomic force microscopy,biological techniques,deformation,elastomers,molecular biophysics,nanobiotechnology}, pages = {133901--3} }, @article{he_polyurethane_2002, title = {Polyurethane molecular stamps for the in situ synthesis of {DNA} microarray}, volume = {13}, number = {9}, journal = {Chinese Chemical Letters}, author = {N. Y. He and Z. C. Liu}, year = {2002}, pages = {883--886} }, @misc{_electro-optic_????, title = {{Electro-Optic} Polymer Films for Reconfigurable Photomask Applications}, url = {http://adsabs.harvard.edu/abs/2007APS..MARX17012F} }, @article{kumar_chemical_2001, title = {Chemical nanoprinting: a novel method for fabricating {DNA} microchips}, volume = {29}, url = {http://nar.oxfordjournals.org/cgi/content/abstract/29/2/e2}, doi = {10.1093/nar/29.2.e2}, abstract = {We have developed a novel cost-effective procedure, namely chemical nanoprinting', for oligonucleotide or {cDNA} chips manufacture. In this thermo-controlled process, the oligonucleotides, covalently attached to a highly loaded master-chip' through disulfide bonds, are chemically transferred to the acrylamide layer mounted on a print-chip'. It is demonstrated here that multiple identical print-chips can be produced from a single master-chip. This duplication process is a few hundreds of times faster than any existing methods and the speed of process and cost incurred are independent of the scale of the {DNA} chips. }, number = {2}, journal = {Nucl. Acids Res.}, author = {Anil Kumar and Zicai Liang}, year = {2001}, pages = {e2} }, @article{smirnova_synthesis_2005, title = {Synthesis of Caged Nucleosides with Photoremovable Protecting Groups Linked to Intramolecular Antennae}, volume = {88}, url = {http://dx.doi.org/10.1002/hlca.200590067}, doi = {10.1002/hlca.200590067}, abstract = {Based on the [2-(2-nitrophenyl)propoxy]carbonyl (nppoc) group, six new photolabile protecting groups (2, 8, 9b, 16b, 25b, and 26), each covalently linked to a {9H-thioxanthen-9-one} {(Tx)} unit functioning as an intramolecular triplet sensitizer, were synthesized. Linkers were introduced between the Me group or the aromatic ring of nppoc and the 2-position of Tx by means of classical organic synthesis combined with Pd catalyzed {C\&bond;C} coupling reactions. The new photolabile protecting groups to be used in light-directed synthesis of {DNA} chips were attached to the {5prime-O-atom} of thymidine via a carbonate linkage, giving rise to the caged nucleosides 7, 11, 13, 19, 20, and 30.}, number = {4}, journal = {Helvetica Chimica Acta}, author = {Joulia Smirnova and Dominik W�ll and Wolfgang Pfleiderer and {Ulrich�E.} Steiner}, year = {2005}, pages = {891--904} }, @article{chuang-yuan_lee_-demand_2007, title = {{On-Demand} {DNA} Synthesis on Solid Surface by Four Directional Ejectors on a Chip}, volume = {16}, issn = {1057-7157}, doi = {{10.1109/JMEMS.2007.901110}}, abstract = {This paper presents a synthesis technique for any random deoxyribonucleic acid {(DNA)} sequences on different substrates such as glass, plastic or silicon by an array of directional droplet ejectors. Any {DNA} sequence can be synthesized by ejecting droplets of {DNA} bases by an ultrasonic transducer having lens with air-reflectors {(LWARs)} that requires no nozzle. The {LWAR} is capable of ejecting liquid droplets around 80 mum in diameter, and reduces the amount of reagents needed for the synthesis from most of conventional microarray techniques. One major advantage of the nozzleless ejector is that it can eject droplets in any direction, so that a spot can be inked by four ejectors (carrying four {DNA} bases) without moving the ejector. The directional ejection of the droplets removes the need for aligning the substrate with the ejector, and minimizes the automation and control circuitry. To demonstrate the {DNA} synthesis capability of the directional droplet ejectors, four {LWAR} ejectors were used to synthesize a 15-mer {5'-CGCCAAGCAGTTCGT-3'} on a substrate surface. This paper describes the concept and scheme of the on-demand {DNA} synthesis (with {MEMS} ejector integrated with microfluidic components) along with experimental results of an actual {DNA} synthesis by four directional droplet ejectors.}, number = {5}, journal = {Microelectromechanical Systems, Journal of}, author = {{Chuang-Yuan} Lee and S. {Kamal-Bahl} and Hongyu Yu and Jae Wan Kwon and Eun Sok Kim}, year = {2007}, keywords = {Acoustic beam focusing,array directional droplet ejectors,deoxyribonucleic acid {(DNA),directional} droplet ejectors,four directional ejectors,lens with air-reflectors,liquid droplets,microarray techniques,nozzleless ejector,ondemand {DNA} synthesis,random deoxyribonucleic acid sequences,solid surface,ultrasonic transducer}, pages = {1130--1139} }, @article{garland_high_2009, title = {High yield detritylation of surface-attached nucleosides with photoacid generated in an overlying solid film: roles of translational diffusion and scavenging}, volume = {7}, url = {http://dx.doi.org/10.1039/b813319k}, abstract = {Conventional solid-phase oligonucleotide synthesis overcomes the reversibility of acid-dependent detritylation by washing away the released dimethoxytrityl cations {(DMT+)} with acid. This option is unavailable if the acid is photogenerated in an overlying solid film, as in the photolithographic fabrication of oligonucleotide arrays on planar surfaces. To overcome the resulting reversibility problem we developed methods of achieving [greater-than-or-equal]98\% detritylation of glass-attached 5[prime or {minute]-O-DMT-thymidine,} a model for 5[prime or {minute]-O-DMT-protected} oligonucleotides, by the photogeneration of trichloroacetic acid in a solid film. Enhanced intrafilm diffusion, insufficient to degrade the photolithographic resolution but enabling {DMT+} to move from its plane of release into the overlying photoacid-generating film, increased detritylation from [less-than-or-equal]30\% to [greater-than-or-equal]98\%. Inclusion of an intrafilm carbocation scavenger such as a triarylsilane hydride converted the detritylation into a time-dependent irreversible process proceeding to [greater-than-or-equal]99\% detritylation within 60 s following brief photoacid generation. Light sensitivity is high, exceeding direct photodeprotection methods by 15-100 fold.}, number = {3}, journal = {Organic \& Biomolecular Chemistry}, author = {Peter B. Garland and Pawel J. Serafinowski}, year = {2009}, pages = {451--459} }, @inproceedings{madigan_lateral_????, title = {Lateral Dye Distribution With {Ink-Jet} Dye Doping of Polymer Organic Light Emitting Diodes}, author = {C. F. Madigan and T. R. Hebner and J. C. Sturm and R. A. Register and S. Troian} }, @article{g_lithographic_2000, title = {Lithographic Techniques for the Fabrication of Oligonucleotide Arrays.}, volume = {13}, issn = {0914-9244}, url = {http://sciencelinks.jp/j-east/article/200020/000020002000A0692981.php}, abstract = {Miniaturized arrays of immobilized oligonucleotide probes have immense potential as tools for the rapid analysis of {DNA} sequences. There are a variety of techniques that can be used to fabricate these arrays including robotic spotting, ink-jet printing, and photolithographic patterning. In this report we will provide an overview of microarray technology and describe recent efforts at developing photoresist based techniques for array fabrication. (author abst.)}, number = {4}, journal = {J Photopolym Sci Technol}, author = {Wallraff G and Hinsberg W and Brock P and Mcgall G}, year = {2000}, pages = {551--558} }, @article{hasenbank_demonstration_2008, title = {Demonstration of multi-analyte patterning using piezoelectric inkjet printing of multiple layers}, volume = {611}, issn = {0003-2670}, url = {http://www.sciencedirect.com/science/article/B6TF4-4RRFNDG-2/2/651313cf487f30c5335027b78777c098}, doi = {10.1016/j.aca.2008.01.048}, abstract = { Patterning substrates with biological reagents is a critical component of biosensor development. Many applications require multi-analyte patterning capabilities, with a need to deposit several species reproducibly with a high degree of precision. We demonstrate a piezoelectric inkjet printing system that is capable of creating sub-millimeter (down to 150 [mu]m) patterns of aqueous and nonaqueous reagents with precise placement for biosensor applications. The size, shape, and density of the patterns may be modified by simple adjustments of the patterning parameters. Using this system, two methods of multi-analyte protein patterning for use in biosensor assays are demonstrated. The first method involves the deposition of multiple proteins directly onto a gold substrate. Specific binding of an antibody to the deposited antigen is demonstrated, although nonspecific adsorption of the antibody may limit the utility of this simple method in quantitative biosensor applications. A second, more sophisticated multi-analyte patterning method involves two sequential patterning steps, consisting of an initial deposition onto gold of a mixed thiol layer to provide oriented binding capabilities in a nonfouling background and a second deposition of multiple biotinylated proteins. Highly specific antibody binding to this patterned multi-analyte surface was demonstrated, with minimal nonspecific adsorption to the surrounding regions. Thus, this method produces high-quality, localized, and customizable sub-millimeter patterns in a nonfouling background for multi-analyte bioassay development.}, number = {1}, journal = {Analytica Chimica Acta}, author = {Melissa S. Hasenbank and Thayne Edwards and Elain Fu and Richard Garzon and T. Fettah Kosar and Michael Look and Afshin {Mashadi-Hossein} and Paul Yager}, month = mar, year = {2008}, keywords = {Inkjet {printing,Multi-analyte,Protein} {patterning,Thiol} patterning}, pages = {80--88} }, @article{kim_deep_2008, title = {Deep blue phosphorescent organic light-emitting diodes using a Si based wide bandgap host and an Ir dopant with electron withdrawing substituents}, volume = {517}, number = {2}, journal = {Thin Solid Films}, author = {S. H. Kim and J. Jang and S. J. Lee and J. Y. Lee}, year = {2008}, pages = {722--726} }, @misc{_photo-removable_2004, title = {{Photo-Removable} Protecting Groups for in Situ {DNA} Microarray Synthesis}, url = {http://www.clinchem.org/cgi/content/extract/50/10/1936}, month = oct, year = {2004}, howpublished = {http://www.clinchem.org/cgi/content/extract/50/10/1936} }, @article{naiser_versatile_2006, title = {Versatile maskless microscope projection photolithography system and its application in light-directed fabrication of {DNA} microarrays}, volume = {77}, url = {http://link.aip.org/link/?RSI/77/063711/1}, doi = {10.1063/1.2213152}, number = {6}, journal = {Review of Scientific Instruments}, author = {Thomas Naiser and Timo Mai and Wolfgang Michel and Albrecht Ott}, month = jun, year = {2006}, keywords = {biological techniques,bio-optics,focal planes,image resolution,micromirrors,molecular biophysics,optical arrays,optical films,optical focusing,optical microscopes,optical projectors,photochemistry,photoresists,spatial light modulators}, pages = {063711--11} }, @article{gulari_light_2003, title = {Light directed massively parallel on-chip synthesis of peptide arrays with {t-Boc} chemistry}, volume = {3}, journal = {Proteomics}, author = {E. Gulari}, year = {2003}, pages = {2135--2141} }, @article{thompson_easy_2001, title = {It's easy to build your own microarrayer!}, volume = {9}, url = {http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TD0-42NRD1F-5&_user=108429&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000059713&_version=1&_urlVersion=0&_userid=108429&md5=a6c9f2055b0bc70618bf9e68e4ee939b}, doi = {{10.1016/S0966-842X(01)01977-1}}, abstract = {Molecular Microbiology, Institute of Food Research, Colney Lane, Colney, Norwich, {UK} {NR4} {7UA} {DNA} microarrays are becoming the tool of choice for microbial gene-expression profiling and genotypic analysis. The construction of a gridding robot for the ‘in-house’ production of microarrays is a choice worth considering, and offers distinct advantages over other options in terms of cost effectiveness and scale. Having built our own robot, we want to dispel some of the myths that might be associated with such a project, as well as provide practical advice for potential builders in the {UK} and Europe. Author Keywords: genomics; microarrays; gridding robot; self-build; printing pins; linear actuators; motors; gasy Subject-index terms: Microbiology Microarrays are becoming the pre-eminent technology for the investigation of functional genomics. Many laboratories and research centres are deciding whether to invest in microarraying technology by setting up ‘in-house’ facilities or purchasing commercial pre-printed arrays, which can cost £500 each. One factor that can influence this decision is that a significant number of microarrays is required to obtain one set of publishable data. It is not possible to re-use microarrays for fluorescent {DNA} applications, and the results from several microarray experiments are required to produce robust data [1]. Microarrays are produced by specialized gridding robots [2], which are readily available from several {US} and European companies for upwards of £50 000. The machines differ in terms of the accessories, which include the type and number of print pins (4–48), the number of slides that can be printed in a single run, and the inclusion of cooled plate stackers, and humidity or temperature controls. An attractive alternative is the construction of your own microarraying robot. This is surprisingly easy, and offers a cheap and effective way to produce microarrays at a density of up to 40 000 spots per microscope slide. The total cost to build this robot is in the region of £18 000 plus the cost of at least 20 printing pins (£100 each). Plans for this robust and accurate basic machine, which was designed by Joe {DeRisi} and Pat Brown at Stanford University, are freely available at: http://cmgm.stanford.edu/pbrown/mguide/ index.html. The site includes clear building instructions, and the details of suppliers of specific parts, as well as the software (free to academic institutions and available at a small cost to industrial concerns) for programming the microarraying robot and the analysis of microarray data. We are currently one of the two institutions within the {UK} to have built our own {DNA} microarrayer according to the Stanford design, the other location being at the {MRC} Toxicology Unit, University of Leicester (http://www.le.ac.uk/cmht/twg1/array-fp.html). The construction of our microarrayer was inspired by a Cold Spring Harbor course attended by {A.T.} from 20 October to 2 November 1999 entitled {‘Making} and Using {DNA} Microarrays’, where a group of 16 participants constructed four microarrayers within two days [3]. This article is intended to address the reservations held by most molecular biologists about pursuing a {DIY} project of this type. We hope to dispel the impression that self-build is an intimidating undertaking. A ‘state of the art’ engineering workshop is certainly not required; all that is needed is a little patience, and some familiarity with the use of a screwdriver and wire stripper. As Joe {DeRisi} says ‘a 14 year old could do it in a few hours’ [4]! The truth behind this comment is that nearly all of the microarrayer components are modular and it is mostly a case of literally bolting them down onto a ‘breadboard’ once they arrive from the suppliers. The amount of expertise required with a wire stripper and screwdriver is no more than that required to wire up a 13 amp electric plug. Some rudimentary computing know-how is also useful for the downloading and installation of the freeware for controlling the arrayer. We found that the most time-consuming part of self-build stemmed from the shipping times of the components, particularly those sourced from the {USA.} We hope to relay some of the lessons we have learned from having constructed a machine in the {UK} and to describe the straightforward adaptation of the machine for use with {UK} and European mains voltage. The central components of the robot are the three custom-assembled linear actuators and motors, which provide {3-D} movement to enable the printing process. The motors are computer controlled and connect to the ‘linear actuators’, which are built in the {USA} by {Parker-Hannifen.} The actuators convert rotary to linear motion and have a positional accuracy of ±2.47 μm. Briefly, microarray production involves the printing of {DNA} onto glass microscope slides that have been coated with a {DNA-binding} substrate and which are laid out onto a platter {(Fig.} 1). The platter carries up to 137 microscope slides, and is positioned by the X-axis actuator so that consecutive slides lie beneath the print head. The print head carries either 16 or 32 hardened steel pins, which are moved by two actuators (the Y and Z axes) to the washing and drying stations, before dipping into a 384-well microtitre plate containing the {DNA} solutions to be printed. The pins tap down and deposit sub-nanolitre amounts of {DNA} solution onto each consecutive slide. Delivery of the custom-built actuators takes around 2–3 months and these should be ordered first, along with the solid base (the breadboard), onto which the actuators and other components are bolted. It is important when ordering the breadboard to specify that it is laid out in imperial measurements. It is also worth remembering that the legs for the breadboard are packed on top of what looked to us like a pallet bottom, but which in fact contains the breadboard itself! A British company Micromech, will carry out the actuator construction (for the Z axis at least) and should be a more rapid supplier than {Parker-Hannifen} for those building in Europe. Alternately, the actuators can be supplied already correctly set up on a breadboard from Western Technology in the {USA;} this option will again take a few months to process. On the Cold Spring Harbor course, the actuators and breadboard were supplied separately. Printing pins are the most crucial variable in the generation of high-density microarrays. The printing pins on the Stanford arrayer are what is known as the ‘quill’ type, and have a thousandth of an inch width slit at the tapered tip of the pin, which wicks up the {DNA} solution. Because the pins tap repeatedly onto the surface of the slides they need to be robust and to be kept free of blockages. We have found the pins produced by Majer Precision to be particularly robust (http://www.majerprecision.com). Alternately, {Die-Tech} also manufacture suitable pins {(DIE-TECH@ix.netcom.com).} We prepare new pins by doing thousands of preliminary taps on a few slides. There is a special ‘test-array’ program included with the Stanford software that permits this before full-scale printing. In our experience, some of the pins that do not work initially will start to print, and others will stop printing. We think this is caused by bending of the prongs on either side of the slit, which seems to affect deposition and might be the result of a very slightly off-centred slit position. Bending of the prongs too far inwards or outwards seems to prevent spot deposition. Occasionally, pins can become blocked with salt deposits or other contaminants and can be cleaned by gently wiping the tips with ethanol or water. Failing this, pins can be inspected under a low-power microscope and carefully unblocked by inserting a 0.001 inch feeler stock {(RS} components cat. no. 572-139) into the slit. Once a set of reliable pins is obtained after a few hours test printing, it should go on to print many thousands of spots consistently. One advantage of using the sturdy Majer Precision pins is that they can be repeatedly sonicated during the wash stage without apparent damage. We recommend ordering twice as many pins as you plan to use for arraying to allow for pins that do not print. Once the motors and linear actuators have been bolted down (a matter of an hour), the wiring of the motors to their respective amplifiers and the ‘breakout box’ can begin. The breakout box is the interface between the computer card and the amplifiers. This is pretty straightforward work consisting of wire stripping and using a small screwdriver to screw the wires into their respective terminals. The {‘Mguide’} {(Pat} Brown's self-build guide on the web) gives careful instruction concerning which coloured wires to put where. The motors themselves are controlled via a {DMC-1739} controller card and it is important to ensure that the computer contains an {ISA} slot for this. The one and only encounter with a soldering iron will be the construction of a small relay box that coordinates the switching on and off of the sonicator and dry stations. A member of our laboratory {(S.L.)} who had no previous experience of soldering managed this task in just 10 min. The wash station sonicating water bath was ordered from the {USA;} however, the Gast vacuum pump connected to the dry station was of {UK} origin. Both items are controlled via the relay box, which is connected via a multi-board adapter to a {110V} step-down transformer, purchased from {RS} components. Thus, it was necessary for us to use a step-up transformer to reconvert the {110V} output from the relay box to the vacuum pump to {240V} {(UK} voltage). Alternatively, a {240V} sonicating water bath of suitable size could be used, and the whole set-up run at {240V} to circumvent the need for a step-up transformer. The suppliers and distributors we used in the {UK} for the electronic and other components are listed in Table 1. The entire building process took around a week, working part-time. To finish off the robot, we had a dust cover made in perspex to fit over the front and back of the arrayer and also a simple cover for the amplifiers and breakout box {(Fig.} 1), the dimensions of which are available from us on request. We house the machine in an air conditioned, {HepA-filtered} room, to minimize dust deposition during microarray printing, and typically maintain the ambient temperature at {18°C.} Overall, we are very pleased with the results of our efforts and the reproducibility of the printed spots is superb, typically between 100–150 μm in diameter. Fig. 2 shows that 484 spots, or features, can be printed from a single pin loaded with {DNA} just once. The main advantages of the Stanford-designed microarrayer lie in its modest cost, robustness, accuracy, simplicity and its ability to print a maximum of 137 slides in one run. The one disadvantage compared with many commercial microarrayers is that it does not have a plate stacker, making it necessary to return to the machine every 30 min or so to change microtitre plates; however, this removes the necessity to have humidity or temperature controls, which are required to prevent evaporation from uncovered plates. So far, our machine has been used to array the Campylobacter jejuni genome, which took around four hours to produce 137 microarrays, each containing 1600 genes. It will shortly be used to array the Escherichia coli K12 and Salmonella typhimurium {LT2} genomes. We hope that this article will encourage potential self-builders, and will be happy to advise on specific issues. We are grateful for support from the {BBSRC} to set up the {IFR} Microarray Facility, for assistance from Bruce Pearson with construction and to Joe {DeRisi,} Pat Brown, Tim Gant and David Judah for their encouragement and advice. We thank David Jones and Barry Murrell for building the dust cover and electronics box. }, number = {4}, journal = {Trends in Microbiology}, author = {Arthur Thompson and Sacha Lucchini and Jay C. D. Hinton}, month = apr, year = {2001}, pages = {154--156} }, @misc{bialic_phototraceur_2008, title = {Phototraceur {UV} à micro-miroirs pour la réalisation de fonctions optiques integrées et diffractives}, url = {http://hal.archives-ouvertes.fr/hal-00358504/}, author = {Emilie Bialic and Melanie Kessels and Isabelle Hardy and Philippe Grosso and Kevin Heggarty and Rafael Torres and Pierre {Pellat-Finet}}, month = oct, year = {2008}, note = {Le sujet concerne la réalisation d'un phototraceur utilisant un écran à micro-miroirs {(DMD} : Digital Micro-mirror Device) fonctionnant dans {l'UV} entre 300 et 400 nm. Ce phototraceur permet la photo-inscription directe dans des polymères de fonctions optiques intégrées et/ou d'éléments diffractifs.}, howpublished = {http://hal.archives-ouvertes.fr/hal-00358504/} }, @misc{_development_????, title = {Development of Photolithography System with Liquid Crystal Device as Active Mask for Synthesizing {DNA} Chips.}, url = {http://sciencelinks.jp/j-east/article/200322/000020032203A0726206.php} }, @article{ruiz_liquid_2001, title = {{LIQUID} {CRYSTAL} {MASK} {FOR} {OPHTHAMOLOGICAL} {LASER} {SURGERY}}, author = {L. {RUIZ} and E. {MATALLANA}}, year = {2001} }, @article{gao_in_2004, title = {In situ synthesis of oligonucleotide microarrays}, volume = {73}, url = {http://dx.doi.org/10.1002/bip.20005}, doi = {10.1002/bip.20005}, abstract = {This contribution presents a brief overall look of the methods for the preparation of various types of {DNA} microarrays and a thorough examination of the methods for in situ synthesis of oligonucleotide microarrays. � 2004 Wiley Periodicals, Inc. Biopolymers, 2004}, number = {5}, journal = {Biopolymers}, author = {Xiaolian Gao and Erdogan Gulari and Xiaochuan Zhou}, year = {2004}, pages = {579--596} }, @article{gurtner_photoelectrophoretic_2000, title = {Photoelectrophoretic Transport and Hybridization of {DNA} Oligonucleotides on Unpatterned Silicon Substrates}, volume = {122}, url = {http://dx.doi.org/10.1021/ja000487b}, doi = {10.1021/ja000487b}, abstract = {We describe a platform for photoelectrophoretic transport and electronic hybridization of fluorescence-labeled {DNA} oligonucleotides in a low conductivity electrolyte. At the core of the platform is a chemically stabilized semiconductor photodiode or photoconductor surface coated with a streptavidinagarose permeation layer. Micro-illumination of this surface generates photoelectrochemical currents that are used to electrophoretically transport and attach biotinylated {DNA} capture strands to arbitrarily selected locations. The same process is then used to transport and electronically hybridize fluorescence-labeled {DNA} target strands to the previously attached capture strands. Signal detection is accomplished either by a fluorescence scanner or a {CCD} camera. This represents a flexible electronic {DNA} assay platform that does not rely on pre-patterned microelectronic arrays.}, number = {36}, journal = {Journal of the American Chemical Society}, author = {Christian Gurtner and Carl F. Edman and Rachel E. Formosa and Michael J. Heller}, year = {2000}, pages = {8589--8594} }, @article{egeland_high-resolution_????, title = {{High-Resolution} Electrochemical In Situ Printing}, author = {R. D. Egeland and E. M. Southern} }, @inproceedings{pawloski_photolithographic_2007, title = {Photolithographic synthesis of high-density {DNA} probe arrays: Challenges and opportunities}, volume = {25}, url = {http://link.aip.org/link/?JVB/25/2537/1}, doi = {10.1116/1.2794325}, booktitle = {J. Vac. Sci. Technol. B}, publisher = {{AVS}}, author = {Adam R. Pawloski and Glenn {McGall} and Robert G. Kuimelis and Dale Barone and Andrea Cuppoletti and Paul Ciccolella and Eric Spence and Farhana Afroz and Paul Bury and Christy Chen and Chuan Chen and Dexter Pao and Mary Le and Becky {McGee} and Elizabeth Harkins and Michael Savage and Sim Narasimhan and Martin Goldberg and Richard Rava and Stephen P. A. Fodor}, month = nov, year = {2007}, keywords = {biomedical {equipment,bioMEMS,molecular} biophysics,photolithography,polymer films}, pages = {2537--2546} }, @article{wll_highly_2006, title = {Highly Efficient Photolabile Protecting Groups with Intramolecular Energy Transfer13}, volume = {45}, url = {http://dx.doi.org/10.1002/anie.200504091}, doi = {10.1002/anie.200504091}, abstract = {No Abstract}, number = {18}, journal = {Angewandte Chemie International Edition}, author = {Dominik W�ll and Julia Smirnova and Wolfgang Pfleiderer and Ulrich E. Steiner}, year = {2006}, pages = {2975--2978} }, @inproceedings{xiao_soft_2001, title = {Soft lithography for oligonucleotide arrays fabrication}, volume = {3}, isbn = {{1094-687X} }, abstract = {A method for fabricating high-density oligonucleotide arrays directed by a set of molecular stamps is reported in this paper. In this method, based on the standard phosphoramidites chemistry protocol, the coupling was conducted under soft lithography. A 20-mer {DNA} microarray with 10,000 probes has been successfully fabricated, which shows the advantages of accurate, reliable operation and low-cost production of high-density {DNA} chips.}, booktitle = {Engineering in Medicine and Biology Society, 2001. Proceedings of the 23rd Annual International Conference of the {IEEE}}, author = {{P.F.} Xiao and {N.Y.} He and {Z.C.} Liu and {Z.H.} Lu}, year = {2001}, keywords = {20-mer {DNA} microarray,accurate reliable operation,arrays,biochemistry,biomolecular electronics,high-density {DNA} chip production,low-cost production,molecular biophysics,molecular stamps set,oligonucleotide arrays fabrication,probes,standard phosphoramidites chemistry protocol}, pages = {3104--3107 vol.3} }, @article{morais_microimmunoanalysisstandard_2007, title = {Microimmunoanalysis on Standard Compact Discs To Determine Low Abundant Compounds}, volume = {79}, number = {20}, journal = {Anal. Chem}, author = {S. Morais and J. Carrascosa and D. Mira and R. Puchades and A. Maquieira}, year = {2007}, pages = {7628--7635} }, @article{beier_production_2000, title = {Production by quantitative photolithographic synthesis of individually quality checked {DNA} microarrays}, volume = {28}, url = {http://nar.oxfordjournals.org/cgi/content/abstract/28/4/e11}, doi = {10.1093/nar/28.4.e11}, abstract = {For {DNA} chip analyses, oligonucleotide quality has immense consequences for accuracy, sensitivity and dynamic range. The quality of chips produced by photolithographic in situ synthesis depends critically on the efficiency of photo-deprotection. By means of base-assisted enhancement of this process using 5'-[2-(2-nitrophenyl)-propyloxycarbonyl]-2'-deoxynucleo{-}side phosphoramidites, synthesis yields improved by at least 12\% per condensation compared to current chemistries. Thus, the eventual total yield of full-length oligonucleotide is increased more than 10-fold in the case of 20mers. Furthermore, the quality of every individual array position was checked quantitatively after synthesis. Subsequently, the quality tested chips were used in successive hybridisation experiments. }, number = {4}, journal = {Nucl. Acids Res.}, author = {Markus Beier and Jorg D. Hoheisel}, month = feb, year = {2000}, pages = {e11} }, @book{yu_phosphorescent_2006, title = {Phosphorescent organic light-emitting diodes}, publisher = {Google Patents}, author = {C. P. Yu and C. W. Ko and T. H. Liu}, year = {2006} }, @article{mcgall_light-directed_1996, title = {Light-directed synthesis of high-density oligonucleotide arrays using semiconductor photoresists}, volume = {93}, url = {http://www.pnas.org/content/93/24/13555.abstract}, doi = {{VL} - 93}, abstract = {High-density arrays of oligonucleotide probes are proving to be powerful new tools for large-scale {DNA} and {RNA} sequence analysis. A method for constructing these arrays, using light-directed {DNA} synthesis with photoactivatable monomers, can currently achieve densities on the order of 10 sequences/cm. One of the challenges facing this technology is to further increase the volume, complexity, and density of sequence information encoded in these arrays. Here we demonstrate a new approach for synthesizing {DNA} probe arrays that combines standard solid-phase oligonucleotide synthesis with polymeric photoresist films serving as the photoimageable component. This opens the way to exploiting high-resolution imaging materials and processes from the microelectronics industry for the fabrication of {DNA} probe arrays with substantially higher densities than are currently available. }, number = {24}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, author = {Glenn {McGall} and Jeff Labadie and Phil Brock and Greg Wallraff and Tiffany Nguyen and William Hinsberg}, month = nov, year = {1996}, pages = {13555--13560} }, @article{gu_new_2008, title = {A new approach to fabricating high density nanoarrays by nanocontact printing}, volume = {26}, url = {http://link.aip.org/link/?JVB/26/1860/1}, doi = {10.1116/1.2998754}, number = {6}, journal = {Journal of Vacuum Science \& Technology B: Microelectronics and Nanometer Structures}, author = {Jian Gu and Xiaoyin Xiao and Bharath R. Takulapalli and Michael E. Morrison and Peiming Zhang and Frederic Zenhausern}, month = nov, year = {2008}, keywords = {atomic force microscopy,molecular biophysics,nanobiotechnology,nanocontacts,nanolithography,ultraviolet lithography}, pages = {1860--1865} }, @article{peng_real-time_2003, title = {Real-time photolithographic technique for fabrication of arbitrarily shaped microstructures}, volume = {42}, url = {http://link.aip.org/link/?JOE/42/477/1}, number = {2}, journal = {Optical Engineering}, author = {Qinjun Peng and Shijie Liu and Yongkang Guo and Bo Chen and Jinglei Du and Yangsu Zeng and Chongxi Zhou and Zheng Cui}, month = feb, year = {2003}, keywords = {diffraction gratings,etching,liquid crystal displays,masks,microlenses,micro-optics,optical fabrication,photolithography,real-time systems}, pages = {477--481} }, @article{fodor_light-directed_1991, title = {Light-directed, spatially addressable parallel chemical synthesis}, volume = {251}, url = {http://www.sciencemag.org/cgi/content/abstract/251/4995/767}, doi = {10.1126/science.1990438}, abstract = {Solid-phase chemistry, photolabile protecting groups, and photolithography have been combined to achieve light-directed, spatially addressable parallel chemical synthesis to yield a highly diverse set of chemical products. Binary masking, one of many possible combinatorial synthesis strategies, yields 2n compounds in n chemical steps. An array of 1024 peptides was synthesized in ten steps, and its interaction with a monoclonal antibody was assayed by epifluorescence microscopy. High-density arrays formed by light-directed synthesis are potentially rich sources of chemical diversity for discovering new ligands that bind to biological receptors and for elucidating principles governing molecular interactions. The generality of this approach is illustrated by the light-directed synthesis of a dinucleotide. Spatially directed synthesis of complex compounds could also be used for microfabrication of devices. }, number = {4995}, journal = {Science}, author = {{SP} Fodor and {JL} Read and {MC} Pirrung and L Stryer and {AT} Lu and D Solas}, month = feb, year = {1991}, pages = {767--773} }, @article{kasif_computational_2002, title = {A computational framework for optimal masking in the synthesis of oligonucleotide microarrays}, volume = {30}, url = {http://nar.oxfordjournals.org/cgi/content/abstract/30/20/e106}, doi = {10.1093/nar/gnf105}, abstract = {High-throughput genomic technologies are revolutionizing modern biology. In particular, {DNA} microarrays have become one of the most powerful tools for profiling global {mRNA} expression in different tissues and environmental conditions, and for detecting single nucleotide polymorphisms. The broad applicability of gene expression profiling to the biological and medical realms has generated expanding demand for mass production of microarrays, which in turn has created considerable interest in improving the cost effectiveness of microarray fabrication techniques. We have developed the computational framework for an optimal synthesis strategy for oligonucleotide microarrays. The problem was introduced by Hubbell et al. Here, we formalize the problem, obtain precise bounds on its complexity and devise several computational solutions. }, number = {20}, journal = {Nucl. Acids Res.}, author = {Simon Kasif and Zhiping Weng and Adnan Derti and Richard Beigel and Charles {DeLisi}}, month = oct, year = {2002}, pages = {e106} }, @article{xiao_improved_2006, title = {An improved gel-based {DNA} microarray method for detecting single nucleotide mismatch}, volume = {27}, url = {http://dx.doi.org/10.1002/elps.200500918}, doi = {10.1002/elps.200500918}, abstract = {{3-D} polyacrylamide gel-based {DNA} microarray platforms provide a high capacity for nucleic acids immobilization and a solution-mimicking environment for hybridization. However, several technological bottlenecks still remain in these platforms, such as difficult microarray preparation and high fluorescent background, which limit their application. In this study, two new approaches have been developed to improve the convenience in microarray preparation and to reduce the background after hybridization. To control the polymerization process, solutions containing acrylamide-modified oligonucleotide, acrylamide, glycerol and ammonium persulfate are spotted onto a functionalized glass slide, and then the slide is transferred to a vacuum chamber with {TEMED,} so that {TEMED} is vaporized and diffused into the spots to induce polymerization. By applying an electric field across a hybridized microarray to remove the nonspecifically bound labeled targets, this approach can solve the problem of high fluorescent background of the gel-based microarray after hybridization. Experimental results show that our immobilization method can be used to construct high quality microarrays and exhibits good reproducibility. Moreover, the polymerization is not affected by {PCR} medium, so that {PCR} products can be used for microarray construction without being treated by commercial purification cartridges. Electrophoresis can improve the signal-to-noise significantly and has the ability to differentiate single nucleotide variation between two homozygotes and a heterozygote. Our results demonstrated that this is a reliable novel method for high-throughput mutation analysis and disease diagnosis.}, number = {19}, journal = {{ELECTROPHORESIS}}, author = {Peng Feng Xiao and Lu Cheng and Yuan Wan and Bei Li Sun and Zao Zao Chen and Sheng You Zhang and Chung Ziu Zhang and Guo Hua Zhou and Zu Hong Lu}, year = {2006}, pages = {3904--3915} }, @article{matson_biopolymer_1995, title = {Biopolymer Synthesis on Polypropylene Supports: Oligonucleotide Arrays}, volume = {224}, issn = {0003-2697}, url = {http://www.sciencedirect.com/science/article/B6W9V-45NHXKT-2Y/2/3bcb780a9f493a04a942fbabce8395c8}, doi = {10.1006/abio.1995.1014}, abstract = { High-density oligonucleotide arrays have been constructed on clear, aminated polypropylene film using conventional phosphoramidite-based synthesis chemistries. A semiautomated 64-channel fluidic chemical delivery system is used to prepare the 64 × 64 array containing 4096 oligonucleotide elements. The completed array has been successfully used in the hybridization and fluorescence {(Streptavidin-FITC)} detection of a biotinylated 18-mer oligonucleotide target complementary to the F508 codon region of the cystic fibrosis transmembrane conductance regulator gene. A hybridization simulation model based upon Nearest Neighbor approximations is used to predict the outcome of the array hybridization experiment.}, number = {1}, journal = {Analytical Biochemistry}, author = {R. S. Matson and J. Rampal and S. L. Pentoney and P. D. Anderson and P. Coassin}, year = {1995}, pages = {110--116} }, @article{zammatteo_comparison_2000, title = {Comparison between Different Strategies of Covalent Attachment of {DNA} to Glass Surfaces to Build {DNA} Microarrays}, volume = {280}, issn = {0003-2697}, url = {http://www.sciencedirect.com/science/article/B6W9V-45FK5G6-FG/2/0f7489d2ad14ecc2d789f48b53dd99d0}, doi = {10.1006/abio.2000.4515}, abstract = { {DNA} microarray is a powerful tool allowing simultaneous detection of many different target molecules present in a sample. The efficiency of the array depends mainly on the sequence of the capture probes and the way they are attached to the support. The coupling procedure must be quick, covalent, and reproducible in order to be compatible with automatic spotting devices dispensing tiny drops of liquids on the surface. We compared several coupling strategies currently used to covalently graft {DNA} onto a glass surface. The results indicate that fixation of aminated {DNA} to an aldehyde-modified surface is a choice method to build {DNA} microarrays. Both the coupling procedure and the hybridization efficiency have been optimized. The detection limit of human cytomegalovirus target {DNA} amplicons on such {DNA} microarrays has been estimated to be 0.01 {nM} by fluorescent detection.}, number = {1}, journal = {Analytical Biochemistry}, author = {Nathalie Zammatteo and Laurent Jeanmart and Sandrine Hamels and Stéphane Courtois and Pierre Louette and Laszlo Hevesi and José Remacle}, month = apr, year = {2000}, keywords = {glass; functionalization; {DNA} probe; microarray}, pages = {143--150} }, @article{huang_solvent_2007, title = {Solvent resistant microfluidic {DNA} synthesizer}, volume = {7}, url = {http://dx.doi.org/10.1039/b613923j}, abstract = {We fabricated a microfluidic {DNA} synthesizer out of perfluoropolyether {(PFPE),} an elastomer with excellent chemical compatibility which makes it possible to perform organic chemical reactions, and synthesized 20-mer oligonucleotides on chip.}, number = {1}, journal = {Lab on a Chip}, author = {Yanyi Huang and Piero Castrataro[double dagger] and {Cheng-Chung} Lee[double dagger] and Stephen R. Quake}, year = {2007}, pages = {24--26} }, @article{liu_optical-data-processing_1985, title = {Optical-data-processing properties of a liquid-crystal television spatial light modulator}, volume = {10}, url = {http://ol.osa.org/abstract.cfm?URI=ol-10-12-635}, doi = {{10.1364/OL.10.000635}}, abstract = {The potential of the extremely inexpensive Radio Shack liquid-crystal television {(LCTV)} as a two-dimensional spatial light modulator has been investigated. The {LCTV} modulates the transmission of coherent or incoherent light and can either be electronically addressed through a microcomputer or optically addressed with a {TV} camera. We have measured the transmission characteristics of the device, examined its diffraction pattern, and tested its use as an input device for an optical correlator. We have discovered that, with proper modifications, it has potential for optical-data-processing applications.}, number = {12}, journal = {Optics Letters}, author = {{Hua-Kuang} Liu and Jeffrey A. Davis and Roger A. Lilly}, month = dec, year = {1985}, pages = {635--637} }, @article{naiser_hybridization_2006, title = {Hybridization to surface-bound oligonucleotide probes: Influence of point defects}, url = {http://arxiv.org/abs/q-bio/0612043}, abstract = {Microarray-based genotyping is based on the high discrimination capability of oligonucleotide probes. For detection of Single Nucleotide Polymorphisms {(SNPs)} single-base discrimination is required. We investigate how various point-mutations, comprising single base mismatches {(MMs),} insertions and deletions, affect hybridization of {DNA-DNA} oligonucleotide duplexes. Employing light-directed in situ synthesis we fabricate {DNA} microarrays with comprehensive sets of cognate point-mutated probes, allowing us to systematically investigate the influence of defect type, position and nearest neighbor effects. Defect position has been identified as the dominating influential factor. This positional effect which is almost identical for the different point-mutation types, is biased from the local sequence environment. The impact of the {MM} type is largely determined by the type of base pair (either {AT} or {CG)} affected by the mismatch. We observe that single base insertions next to like-bases result in considerably larger hybridization signals than insertions next to nonidentical bases. The latter as well as the distinct position dependence could be explained by a kinetic zipper model in which point defects represent a barrier for the rapid closure of the {DNA} duplex.}, journal = {q-bio/0612043}, author = {Thomas Naiser and Oliver Ehler and Timo Mai and Wolfgang Michel and Albrecht Ott}, month = dec, year = {2006}, keywords = {Quantitative Biology - {Biomolecules,Quantitative} Biology - Genomics} }, @misc{ruiz_controllable_????, title = {Controllable liquid crystal matrix mask particularly suited for performing ...}, url = {http://www.google.com/patents?hl=en&lr=&vid=USPATAPP10207073&id=nvOGAAAAEBAJ&oi=fnd&dq=%22active+mask%22+photolithography}, abstract = {A system and method particularly suited for controlled ablation of the cornea, using ultraviolet laser radiation, with the cornea sculpturing action resulting from a computer driven digital programmed distribution of excimer flux density across a controllable liquid crystal matrix mask to achieve a desired volume and shape of ablation for the correction of the curvature of the cornea. The optical mask, in one embodiment, is based on an arrayable matrix of individual optical pixel cells with two optical states between fully transparent to fully opaque or mirror like to the {UV} light. The system provides a highly versatile system for correcting known corneal defects in both regular and irregular corneas by simply executing computer customized patterns in very short time and with great precision and detail. }, author = {Luis Antonio Ruiz and Eduardo Matallana}, note = {{U.S.} Classification: 606005000 ; International Classification: {A61B018/20} } }, @article{takahashii_photochemical/chemical_2002, title = {A photochemical/chemical direct method of synthesizing high-performance deoxyribonucleic acid chips for rapid and parallel gene analysis}, volume = {83}, issn = {0925-4005}, url = {http://www.sciencedirect.com/science/article/B6THH-44TCYXY-1/2/7644f95c3774181c8312031f25d36668}, doi = {{10.1016/S0925-4005(01)01030-9}}, abstract = { We propose a new method of synthesizing perfect sets of probe deoxyribonucleic acid {(DNA)} on a chip to produce high-performance {DNA} chips. Two different methods of direct synthesis are combined to generate single strands of probe {DNA} on the chip's surface. The first is an area-specific photosensitive synthesis of {DNA} that exploits photolithographic techniques. The other is a non-photosensitive synthesis of {DNA.} This is a much more reliable method of synthesis and is used for the remaining sequences of probe {DNA,} i.e. those outside the photosynthesis region. In the synthesis procedure, photosensitive reagents are only used to make certain variations to the probe {DNA} and areas with several kinds of probe {DNA} (4 to 16 nucleotides in length) were synthesized on each 50 [mu]m2 of the probe. We examined the application of our {DNA} chip to single-nucleotide polymorphism {(SNP)} analysis, which is used to check for the mutant promoters of liver cancer. We found that no non-specific signals from a hybridization reaction of the sample {DNA} variants appeared and that this {DNA} chip successfully discriminated slight differences in genomic {(DNA)} information at the single base-pair level.}, number = {1-3}, journal = {Sensors and Actuators B: Chemical}, author = {Kazunori Takahashii and Kohji Seio and Mitsuo Sekine and Okio Hino and Masayoshi Esashi}, month = mar, year = {2002}, keywords = {{DNA} {chip,Photochemical} {synthesis,Photolithography,Photosensitive} {reagent,Polymorphism,SNP} analysis}, pages = {67--76} }, @phdthesis{chow_photoelectrochemical_2008, title = {Photoelectrochemical Synthesis of {Low-Cost} {DNA} Microarrays}, school = {Massachusetts Institute of Technology}, author = {B. Y. Chow}, year = {2008} }, @article{negrete_step-and-scan_2008, title = {Step-and-scan maskless lithography for ultra large scale {DNA} chips}, volume = {85}, issn = {0167-9317}, url = {http://www.sciencedirect.com/science/article/B6V0W-4RMNYCM-5/2/fd0f790433ae064534e9e463aa2f2a66}, doi = {10.1016/j.mee.2008.01.014}, abstract = { A maskless photolithography test bed was constructed to examine the requirements for stepper-based synthesis of Ultra Large Scale {DNA} chips {(ULS-DNA} chips). The test bed is based on a microscope optical layout with a 5 × reduction imaging lens and micro/nano controlled staging at the image plane. Spatial light modulation is enabled by a Digital Micromirror Device {(Texas} Instruments {DMD} {0.7XGA)} and the positioning system is composed of a piezoelectric nano-positioner {(nPoint} Inc., Madison, {WI)} mounted on a high precision linear-motor stage {(Newport} Corp., Irvine, {CA).} With this test bed we examined the requirements of overlay and alignment in a stepper-based {DNA} microarray synthesis system. We demonstrated multi-field chip synthesis with a spot size of 3.15 [mu]m at the 5 × reduction. All tests were verified by standard hybridization, and fluorescence microscopy. In addition to our demonstration of step-and-scan lithography for {DNA} chip synthesis, we drafted and modeled an imaging optic for a production scale tool capable of synthesizing {DNA} chips containing up to 20 million pixels.}, number = {5-6}, journal = {Microelectronic Engineering}, author = {Omar D. Negrete and Franco Cerrina}, year = {2008}, keywords = {{DNA} {microarrays,DNA} {synthesis,Maskless} {photolithography,Oligonucleotide} {synthesis,Overlay}}, pages = {834--837} }, @misc{_pholed_????, title = {{PHOLED} - Wikipedia, the free encyclopedia}, url = {http://en.wikipedia.org/wiki/PHOLED} }, @article{bhler_new_2004, title = {New Types of Very Efficient Photolabile Protecting Groups Based upon the {[2-(2-Nitrophenyl)propoxy]carbonyl} {(NPPOC)} Moiety}, volume = {87}, url = {http://dx.doi.org/10.1002/hlca.200490060}, doi = {10.1002/hlca.200490060}, abstract = {Based upon the photolabile [2-(2-nitrophenyl)propoxy]carbonyl group {(NPPOC),} a large number of modified 2-(2-nitrophenyl)propanol derivatives substituted at the phenyl ring (see 23-34 and 57-76) as well as at the side-chain (see 85-92 and 95-98) were synthesized to improve the photoreactivity of this new type of photolabile entity. The phenyl moiety was also exchanged by the naphthalenyl group (see 102, 103, 105, 108, 110, 113, and 114), the thienyl substituent (see 115, 117, 118, and 120), and the benzothienyl substituent (see 121). The 2-(2-nitroaryl- and heteroaryl)propanols were converted with diphosgene into the corresponding carbonochloridates, which reacted subsequently with thymidine to the thymidine 5prime-(protected carbonates) 123-178 as the main reaction products. In several cases, the corresponding 3prime-carbonates and 3prime,5prime-dicarbonates 179-212 were also isolated and characterized. Photolysis studies under standardized conditions (see Table) indicated that the rate of photocleavage varies in a broad range depending on the substituents. So far, the thymidine 5prime-[2-(5-halo-2-nitrophenyl)propyl carbonates] 127-129, 5prime-[2-(nitro[1,1prime-biphenyl]3-yl)propyl carbonates] 136-139, 5prime-{2-[2-nitro-5-(thianthren-1-yl)phenyl]propyl carbonate} (140), 5prime-[2-(5-naphthalenyl-2-nitrophenyl)propyl carbonates] 141 and 142, and 5prime-[2-(2-nitro-5-thienylphenyl)propyl carbonates] 143 and 144 showed the best properties regarding fast and uniform deprotection. Since the nucleobases of 213-215 do not influence the photocleavage features, in general, the new type of photolabile building blocks allows in form of their 3prime-phosphoramidites the photolithographic formation of high-quality biochips.}, number = {3}, journal = {Helvetica Chimica Acta}, author = {Sigrid B�hler and Irene Lagoja and Heiner Giegrich and {Klaus-Peter} Stengele and Wolfgang Pfleiderer}, year = {2004}, pages = {620--659} }, @article{chen_controlling_????, title = {Controlling Oligonucleotide Surface Density in {Light-Directed} {DNA} Array Fabrication}, volume = {0}, url = {http://dx.doi.org/10.1021/la9000297}, doi = {10.1021/la9000297}, abstract = {Over the past two decades high-density {DNA} arrays have developed into a central technology for nucleic acid analyses. Important application areas include whole-genome gene expression studies, high throughput analyses of single nucleotide polymorphisms, and, most recently, the determination of binding site specificities for transcription factors and other critical elements involved in gene regulation. A key parameter in the performance of {DNA} arrays is the density of the surface-bound oligonucleotides, which strongly affects both thermodynamic and kinetic aspects of {DNA} hybridization. In this report, we describe an approach for the control of oligonucleotide density in photolithographically fabricated {DNA} arrays, based upon a controlled {UV} light deprotection procedure. Modulation of the {UV} exposure permits a desired degree of deprotection of surface synthesis sites; a subsequent capping reaction to inactivate the exposed sites leaves only a desired fraction of active sites remaining for synthesis, corresponding to a lower oligonucleotide density. It is shown that the procedure is reasonably general, in that it is readily transferable to alternative substrate materials with similar results.}, number = {0}, journal = {Langmuir}, author = {Siyuan Chen and Margaret F. Phillips and Franco Cerrina and Lloyd M. Smith} }, @article{efron_silicon_1985, title = {The silicon liquid-crystal light valve}, volume = {57}, url = {http://link.aip.org/link/?JAP/57/1356/1}, doi = {10.1063/1.334487}, number = {4}, journal = {Journal of Applied Physics}, author = {U. Efron and J. Grinberg and P. O. Braatz and M. J. Little and P. G. Reif and R. N. Schwartz}, month = feb, year = {1985}, keywords = {{DATA} {PROCESSING,DESIGN,DISPLAY} {DEVICES,FABRICATION,LIQUID} {CRYSTALS,OPERATION,OPTICAL} {MODULATORS,OPTOELECTRONIC} {DEVICES,PERFORMANCE,PHOTOCONDUCTORS,PHOTOSENSITIVITY,SILICON,USES}}, pages = {1356--1368} }, @misc{_organic_????, title = {Organic light-emitting diode - Wikipedia, the free encyclopedia}, url = {http://en.wikipedia.org/wiki/Organic_light-emitting_diode} }, @article{pease_light-generated_1994, title = {Light-generated oligonucleotide arrays for rapid {DNA} sequence analysis}, volume = {91}, url = {http://www.pnas.org/content/91/11/5022.abstract}, doi = {{VL} - 91}, abstract = {In many areas of molecular biology there is a need to rapidly extract and analyze genetic information; however, current technologies for {DNA} sequence analysis are slow and labor intensive. We report here how modern photolithographic techniques can be used to facilitate sequence analysis by generating miniaturized arrays of densely packed oligonucleotide probes. These probe arrays, or {DNA} chips, can then be applied to parallel {DNA} hybridization analysis, directly yielding sequence information. In a preliminary experiment, a 1.28 x 1.28 cm array of 256 different octanucleotides was produced in 16 chemical reaction cycles, requiring 4 hr to complete. The hybridization pattern of fluorescently labeled oligonucleotide targets was then detected by epifluorescence microscopy. The fluorescence signals from complementary probes were 5-35 times stronger than those with single or double base-pair hybridization mismatches, demonstrating specificity in the identification of complementary sequences. This method should prove to be a powerful tool for rapid investigations in human genetics and diagnostics, pathogen detection, and {DNA} molecular recognition. }, number = {11}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, author = {A C Pease and D Solas and E J Sullivan and M T Cronin and C P Holmes and S P Fodor}, month = may, year = {1994}, pages = {5022--5026} }, @article{beier_analysis_2002, title = {Analysis of {DNA-microarrays} produced by inverse in situ oligonucleotide synthesis}, volume = {94}, issn = {0168-1656}, url = {http://www.sciencedirect.com/science/article/B6T3C-44W2K4N-2/2/281bd839bfea5d1678a46ac4a57f6451}, doi = {{10.1016/S0168-1656(01)00416-3}}, abstract = { {5'-Phosphoramidites} protected by 2-nitrophenylethyl {(NPE)} and 2-(4-nitrophenyl)ethoxy carbonyl {(NPEOC)} functions were employed for in situ synthesis of oligonucleotides in 5'--{\textgreater}3' direction on flat glass surfaces. By this inverse synthesis format, the oligonucleotides are attached to the solid support via their 5'-ends while the free 3'-hydroxyl groups are available as substrates for enzymatic reactions such as elongation by polymerases, thereby adding another feature to the portfolio of chip-based applications. Having a fluorescence dye present at the first base during synthesis, the quality of the oligonucleotides was analysed quantitatively by capillary electrophoresis after release from the solid support. With about 95\% yield per condensation, it was found to be equivalent to synthesis results achieved on {CPG} support. The chip-bound oligonucleotides could be extended enzymatically upon hybridisation of a {DNA-template.} Surprisingly, however, only 63\% of the oligonucleotides were elongated in polymerase reactions, while oligonucleotides that were released from the support behaved normally in standard {PCR} amplifications. This rate of 63\% nevertheless compares favourably with an extension rate of only 50\%, which was achieved under identical conditions, if pre-fabricated oligonucleotides of identical sequence had been spotted to the glass support.}, number = {1}, journal = {Journal of Biotechnology}, author = {Markus Beier and Jörg D. Hoheisel}, month = mar, year = {2002}, keywords = {In situ {synthesis,Oligonucleotide} {arrays,Primer} extension}, pages = {15--22} }, @article{he_novel_2007, title = {A novel strategy for in situ maskless synthesis of biochips: Self-driving micro-fluid porous type printing {(SMPTP)}}, volume = {18}, issn = {1001-8417}, url = {http://www.sciencedirect.com/science/article/B8G3X-4MWH8TN-16/2/cccde4e23de5d4d31b58e1cab162df3f}, doi = {10.1016/j.cclet.2006.11.015}, abstract = { A novel maskless technique, self-driving micro-fluid porous type printing {(SMPTP),} was reported to in situ synthesize oligonucleotide arrays on glass slide, which has the merits of low cost, high quality and simple craft. In {SMPTP} for fabricating gene-chips, porous fiber tubes with a number of nanometric or micron channels functioned as "active letters" and were assembled in designed patterns, which are identical to the distribution of monomers in each layer of the array, and four patterns were needed for each layer. By means of capillarity, the synthesis solution was automatically taken into porous tubes assembled in a printing plate and reached the surface. An oligonucleotide array of 160 features with four different 15-mer probes was in situ synthesized using this technique. The four specific oligonucleotide probes, including the matched and the mismatched by the fluorescent target sequence, gave obviously different hybridization fluorescent signals.}, number = {1}, journal = {Chinese Chemical Letters}, author = {Nong Yue He and Ya Fei Guo and Song Li and {Jian-Xin} Tang}, year = {2007}, keywords = {{Biochips,DNA} {microarrays,In} situ {synthesis,Oligonucleotide,Typography}}, pages = {111--114} }, @article{jeon_mask-free_2005, title = {Mask-free photolithographic exposure using a matrix-addressable micropixellated {AlInGaN} ultraviolet light-emitting diode}, volume = {86}, url = {http://link.aip.org/link/?APL/86/221105/1}, doi = {10.1063/1.1942636}, number = {22}, journal = {Applied Physics Letters}, author = {C. W. Jeon and E. Gu and M. D. Dawson}, month = may, year = {2005}, keywords = {aluminium compounds,etching,gallium {compounds,III-V} semiconductors,indium compounds,light emitting diodes,microlenses,optical polymers,photoresists,ultraviolet sources,wide band gap semiconductors}, pages = {221105--3} }, @article{srivannavit_design_2004, title = {Design and fabrication of microwell array chips for a solution-based, photogenerated acid-catalyzed parallel oligonuclotide {DNA} synthesis}, volume = {116}, issn = {0924-4247}, url = {http://www.sciencedirect.com/science/article/B6THG-4CHJ7XD-6/2/dff2ec46d186058b492506264745f6c9}, doi = {10.1016/j.sna.2004.04.025}, abstract = { Development of synthesis methods using high yield acid-labile rather than photolabile group protected monomers is desirable to produce microarrays of superior quality, general adaptability and reduced cost of genetic research. However, using solution photochemistry for acid-labile deprotection requires the reaction sites being isolated from each other to prevent diffusion of reagents during a photolytic reaction. We present fabrication methods of two types of microwell array chips with different isolation strategies for carrying out parallel oligonucleotide {DNA} {(oDNA)} synthesis in the liquid phase: electroplated microwell array chips with an isolation wall and a mechanical sealing, and etched patterned microwell array chips with surface tension isolation. Both surface and bulk micromachining technologies were used for fabrication of those chips. We also discuss various problems regarding fabrication and use. The validated fidelity from the single mismatch detection of oligonucleotide {DNA} microwell array chips is also given to prove successful isolation of the liquid during a photolytic reaction.}, number = {1}, journal = {Sensors and Actuators A: Physical}, author = {Onnop Srivannavit and Mayurachat Gulari and Erdogan Gulari and Eric {LeProust} and Jean Philippe Pellois and Xiaolian Gao and Xiaochuan Zhou}, month = oct, year = {2004}, keywords = {{Micromachining,Microwell,Oligonucleotide} {DNA} {microarray,Photogenerated} acid}, pages = {150--160} }, @article{chakra_new_2008, title = {A new instrument for automated microcontact printing with stamp load adjustment}, volume = {79}, url = {http://link.aip.org/link/?RSI/79/064102/1}, doi = {10.1063/1.2936259}, number = {6}, journal = {Review of Scientific Instruments}, author = {Elie Bou Chakra and Benjamin Hannes and Gilles Dilosquer and Colin D. Mansfield and Michel Cabrera}, month = jun, year = {2008}, keywords = {pneumatic actuators}, pages = {064102--9} }, @article{sullivan_forced_????, title = {Forced Peptide Synthesis in Nanoscale Confinement under Elastomeric Stamps*}, author = {T. P. Sullivan and M. L. van Poll and P. Y. W. Dankers and W. T. S. Huck} }, @article{choi_high-resolution_2004, title = {High-resolution 128 x 96 nitride microdisplay}, volume = {25}, issn = {0741-3106}, doi = {{10.1109/LED.2004.826541}}, abstract = {Matrix-addressable arrays of {InGaN} micro-light-emitting diodes with 128 × 96 pixels and a resolution of 1200 dpi have been fabricated using a novel "sloped sidewall" process. The devices have been fabricated on {InGaN} blue and green wafers, emitting light at the wavelengths of 468 and 508 nm, respectively. A simple circuit, which enables the display of an arrow pattern with ∼60\% of the pixels turned on, was used for device testing. At an injection current of 60 {mA,} the devices deliver 3.3 (blue) and 2.4 {mW} (green) of output power, corresponding to a luminance of more than 30 000 Cd/m2. These high-brightness and highly versatile devices are certainly an attractive form of emissive micro-display.}, number = {5}, journal = {Electron Device Letters, {IEEE}}, author = {{H.W.} Choi and {C.W.} Jeon and {M.D.} Dawson}, year = {2004}, keywords = {2.4 {mW,3.3} {mW,468} nm,508 nm,60 {mA,blue} wafers,device testing,emitting light,green {wafer,III-V} {semiconductors,InGaN,injection} current,light-emitting diode,light emitting diodes,luminance,matrix-addressable arrays,microdisplays,micro-light-emitting diodes,nitride microdisplay,semiconductor device manufacture,semiconductor device testing,sloped sidewall process}, pages = {277--279} }, @article{leproust_characterization_2001, title = {Characterization of oligodeoxyribonucleotide synthesis on glass plates}, volume = {29}, url = {http://nar.oxfordjournals.org/cgi/content/abstract/29/10/2171}, doi = {10.1093/nar/29.10.2171}, abstract = {Achieving high fidelity chemical synthesis on glass plates has become increasingly important, since glass plates are substrates widely used for miniaturized chemical and biochemical reactions and analyses. {DNA} chips can be directly prepared by synthesizing oligonucleotides on glass plates, but the characterization of these micro-syntheses has been limited by the sub-picomolar amount of material available. Most {DNA} chip syntheses have been assayed using in situ coupling of fluorescent molecules to the {5'-OH} of the synthesized oligonucleotides. We herein report a systematic investigation of oligonucleotide synthesis on glass plates with the reactions carried out in an automated {DNA} synthesizer using standard phosphoramidite chemistry. The analyses were performed using {32P} gel electrophoresis of the oligonucleotides cleaved from glass plates to provide product distribution profiles according to chain length of oligonucleotides. {5'-Methoxythymidine} was used as the chain terminator, which permits assay of coupling reaction yields as a function of chain length growth. The results of this work reveal that a major cause of lower fidelity synthesis on glass plates is particularly inefficient reactions of the various reagents with functional groups close to glass plate surfaces. These problems cannot be detected by previous in situ fluorescence assays. The identification of this origin of low fidelity synthesis on glass plates should help to achieve improved synthesis for high quality oligonucleotide microarrays. }, number = {10}, journal = {Nucl. Acids Res.}, author = {Eric {LeProust} and Hua Zhang and Peilin Yu and Xiaochuan Zhou and Xiaolian Gao}, month = may, year = {2001}, pages = {2171--2180} }, @article{cleary_production_2004, title = {Production of complex nucleic acid libraries using highly parallel in situ oligonucleotide synthesis}, volume = {1}, issn = {1548-7091}, url = {http://dx.doi.org/10.1038/nmeth724}, doi = {10.1038/nmeth724}, number = {3}, journal = {Nat Meth}, author = {Michele A Cleary and Kristopher Kilian and Yanqun Wang and Jeff Bradshaw and Guy Cavet and Wei Ge and Amit Kulkarni and Patrick J Paddison and Kenneth Chang and Nihar Sheth and Eric Leproust and Ernest M Coffey and Julja Burchard and W Richard {McCombie} and Peter Linsley and Gregory J Hannon}, month = dec, year = {2004}, pages = {241--248} }, @article{egeland_electrochemically_2005, title = {Electrochemically directed synthesis of oligonucleotides for {DNA} microarray fabrication}, volume = {33}, url = {http://nar.oxfordjournals.org/cgi/content/abstract/33/14/e125}, doi = {10.1093/nar/gni117}, abstract = {We demonstrate a new method for making oligonucleotide microarrays by synthesis in situ. The method uses conventional {DNA} synthesis chemistry with an electrochemical deblocking step. Acid is delivered to specific regions on a glass slide, thus allowing nucleotide addition only at chosen sites. The acid is produced by electrochemical oxidation controlled by an array of independent microelectrodes. Deblocking is complete in a few seconds, when competing side-product reactions are minimal. We demonstrate the successful synthesis of 17mers and discrimination of single base pair mismatched hybrids. Features generated in this study are 40 {micro}m wide, with sharply defined edges. The synthetic technique may be applicable to fabrication of other molecular arrays. }, number = {14}, journal = {Nucl. Acids Res.}, author = {Ryan D. Egeland and Edwin M. Southern}, month = aug, year = {2005}, pages = {e125} }, @article{bhushan_light-directed_2006, title = {Light-directed maskless synthesis of peptide arrays using photolabile amino acid monomers}, volume = {4}, issn = {1477-0520}, url = {http://www.ncbi.nlm.nih.gov/pubmed/16688328}, doi = {10.1039/b601390b}, abstract = {Novel photolabile amino acid monomers for photolithographic solid-phase peptide synthesis has been developed and a method for the maskless synthesis of individually addressable peptide microarrays using new building blocks has been described; these peptide microarrays are suitable for repetitive epitope-binding assays.}, number = {10}, journal = {Organic \& Biomolecular Chemistry}, author = {Kumar R Bhushan}, month = may, year = {2006}, note = {{PMID:} 16688328}, keywords = {Amino {Acids,Peptides,Photochemistry,Protein} Array {Analysis,Protein} Interaction Mapping}, pages = {1857--9} }, @misc{_gene_2002, title = {Gene Expression Analysis Using Oligonucleotide Arrays Produced by Maskless Photolithography}, url = {http://genome.cshlp.org/content/12/11/1749.abstract}, month = nov, year = {2002}, howpublished = {http://genome.cshlp.org/content/12/11/1749.abstract} }, @article{chung-hoon_lee_single_2004, title = {Single microdroplet ejection using an ultrasonic longitudinal mode with a {PZT/tapered} glass capillary}, volume = {51}, issn = {0885-3010}, doi = {{10.1109/TUFFC.2004.1367493}}, abstract = {We have developed an ultrasonic {PZT/tapered} glass capillary resonant actuator that can eject a single droplet every acoustic cycle without also generating satellite droplets. The mechanism of the actuation is resonant longitudinal motion-induced squeezing of a tapered volume. The actuator is driven at 160 {kHz} and requires voltages less than 2 Vpp to operate. In this paper, the droplet generation of isopropanol and water mixtures, which have different densities, viscosities, and surface tensions, is investigated. It is determined that the geometrical squeezing mechanism and the ejected jet breakup makes the droplet size independent of frequency, but more a function of the ejecting orifice diameter that is much smaller than the capillary wavelength.}, number = {11}, journal = {Ultrasonics, Ferroelectrics and Frequency Control, {IEEE} Transactions on}, author = {{Chung-Hoon} Lee and A. Lal}, year = {2004}, keywords = {160 {kHz,acoustic} cycle,actuation mechanism,density,droplet generation,geometrical squeezing mechanism,isopropanol,jets,lead compounds,microdroplet {ejection,PbZrO3TiO3,piezoceramics,piezoelectric} {actuators,PZT,resonant} longitudinal motion-induced squeezing,surface tensions,ultrasonic devices,ultrasonic longitudinal mode,ultrasonic {PZT/tapered} glass capillary resonant actuator,viscosity,water mixtures}, pages = {1514--1522} }, @article{lausted_posam:fast_2004, title = {{POSaM:} a fast, flexible, open-source, inkjet oligonucleotide synthesizer and microarrayer}, volume = {5}, issn = {1465-6906}, url = {http://genomebiology.com/2004/5/8/R58}, doi = {10.1186/gb-2004-5-8-r58}, abstract = {{DNA} arrays are valuable tools in molecular biology laboratories. Their rapid acceptance was aided by the release of plans for a pin-spotting microarrayer by researchers at Stanford. Inkjet microarraying is a flexible, complementary technique that allows the synthesis of arrays of any oligonucleotide sequences de novo. We describe here an open-source inkjet arrayer capable of rapidly producing sets of unique 9,800-feature arrays.}, number = {8}, journal = {Genome Biology}, author = {Christopher Lausted and Timothy Dahl and Charles Warren and Kimberly King and Kimberly Smith and Michael Johnson and Ramsey Saleem and John Aitchison and Lee Hood and Stephen Lasky}, year = {2004}, pages = {R58} }, @article{pirrung_to_2002, title = {How to Make a {DNA} Chip}, volume = {41}, url = {http://dx.doi.org/10.1002/1521-3773(20020415)41:8<1276::AID-ANIE1276>3.0.CO;2-2}, doi = {{10.1002/1521-3773(20020415)41:8{\textless}1276::AID-ANIE1276{\textgreater}3.0.CO;2-2}}, abstract = {Microarrays are one of the hottest areas in biological research today. Microarrays have been mostly applied to nucleic acid analysis, specifically to the assessment of which genes are being expressed and at what level. Early microarrays were prepared by using photolithographic methods, which were more commonly used for integrated circuit (ldquocomputer chiprdquo) production. Hence the colloquial term {ldquoDNA} chiprdquo came into being. The completion of the sequencing of the human genome and that of many other organisms makes the determination of gene function an important next step in understanding the role of {DNA} in the processes of life. {DNA} microarrays are an excellent tool to address this question because their numerous probe sites enable the analysis of many genes simultaneously. With good experience in this initial use, many further applications of microarrays are being developed, including genotyping in research and genetic diagnosis in medicine. {DNA} microarrays have made abundantly clear the power of vast parallelism in biological analysis, which is raising interest in other types of microarrays (small-molecule, protein). Many applications for {DNA} microarrays have been developed and clearly many more will emerge through the creativity of the scientists who use them. In early studies, users produced their own microarrays. The apparent power of microarrays has demanded improvements in production methods, and technologies from physical sciences and engineering are now being applied to {DNA} chips. Many branches of chemistry can contribute to improved methods: from synthetic chemistry (to attach or prepare {DNA),} to the physical chemistry of surfaces, to analytical chemistry (to assess surface reactions).}, number = {8}, journal = {Angewandte Chemie International Edition}, author = {Michael C. Pirrung}, year = {2002}, pages = {1276--1289} }, @article{chan-wook_jeon_high-density_2004, title = {High-density matrix-addressable {AlInGaN-based} 368-nm microarray light-emitting diodes}, volume = {16}, issn = {1041-1135}, doi = {{10.1109/LPT.2004.835626}}, abstract = {We report on the fabrication of ultraviolet {(UV)} microarray light-emitting diodes, toward applications including mask-free photolithographic exposure. Devices with 64 × 64 elements have been fabricated in matrix-addressed format, generating directed output powers of up to 1 {μW} per 20-μm-diameter element at less than {1.0-mA} drive current. The resistance of each elemental device was found to depend strongly on the {n-GaN} stripe length. The center wavelength of the emission was measured to be 368 nm, which is very close to that of an i-line (365 nm) {UV} light source. To our knowledge, this is the first report detailing the fabrication and performance of such devices operating in the {UV.}}, number = {11}, journal = {Photonics Technology Letters, {IEEE}}, author = {{Chan-Wook} Jeon and Hoi Wai Choi and E. Gu and {M.D.} Dawson}, year = {2004}, keywords = {1 {muW,20} mum,365 mum,368 {nm,AlInGaN,AlInGaN-based} light-emitting diodes,aluminium compounds,driver circuits,gallium compounds,high-density light-emitting {diodes,III-V} semiconductors,i-line {UV} light source,indium compounds,light-emitting diode fabrication,light emitting diodes,mask-free exposure,matrix-addressable light-emitting diodes,matrix-addressed format,matrix driver circuit,microarray light-emitting diodes,micro-optics,optical arrays,optical fabrication,photolithographic exposure,photolithography,ultraviolet light-emitting diodes}, pages = {2421--2423} }, @article{garland_effects_2002, title = {Effects of stray light on the fidelity of photodirected oligonucleotide array synthesis}, volume = {30}, url = {http://nar.oxfordjournals.org/cgi/content/abstract/30/19/e99}, doi = {10.1093/nar/gnf098}, abstract = {Fabrication of high density oligonucleotide arrays using metal on glass photolithographic masks is inflexible and expensive. Maskless methods using computer-controlled projection have been proposed and implemented, but associated stray light effects on photodirected oligonucleotide synthesis and their analysis have not been reported. We have developed a theoretical approach: it predicts that the stray light content of the output of digital micromirror devices and other spatial light modulators of similar performance (contrast ratio [{\textasciitilde}]400) will cause extensive random base insertions. For example, use of a digital micromirror device for synthesis of a 20mer array will result in the majority of oligonucleotide chains being 21mers or 22mers. This chain lengthening effect of stray light would not be preventable when synthesis involves a directly photosensitive 5'-blocking group. If the 5'-blocking group is acid labile and released with photogenerated acid, the presence of low concentrations of weak base will prevent the effect of stray light. We have demonstrated experimentally the anticipated chain lengthening effect of stray light on photoacid-dependent synthesis of oligonucleotides and prevention of the effect by low concentrations of n-octylamine. The application of these findings should facilitate the development of maskless fabrication and availability of high density and high fidelity user-designed arrays for research applications. }, number = {19}, journal = {Nucl. Acids Res.}, author = {Peter B. Garland and Pawel J. Serafinowski}, month = oct, year = {2002}, pages = {e99} }, @inproceedings{shimoda_multicolor_1999, title = {Multicolor pixel patterning of light-emitting polymers by ink-jet printing}, volume = {30}, booktitle = {{SID} {INTERNATIONAL} {SYMPOSIUM} {DIGEST} {OF} {TECHNICAL} {PAPERS}}, publisher = {{SOCIETY} {FOR} {INFORMATION} {DISPLAY}}, author = {T. Shimoda and S. Kanbe and H. Kobayashi and S. Seki and H. Kiguchl and I. Yudasaka and M. Kimura and S. Miyashlta and R. H. Friend and J. H. Burroughes}, year = {1999}, pages = {376--381} }, @article{walbert_photolabile_2001, title = {Photolabile Protecting Groups for Nucleosides: Mechanistic Studies of the {2-(2-Nitrophenyl)ethyl} Group}, volume = {84}, url = {http://dx.doi.org/10.1002/1522-2675(20010613)84:6<1601::AID-HLCA1601>3.0.CO;2-S}, doi = {{10.1002/1522-2675(20010613)84:6{\textless}1601::AID-HLCA1601{\textgreater}3.0.CO;2-S}}, abstract = {The photochemistry of several 2-(2-nitrophenyl)ethyl-caged compounds including caged thymidine nucleosides was studied by nanosecond laser flash photolysis and stationary illumination experiments with quantitative {HPLC} analysis for quantum yields and product distribution. Effects of solvent basicity and acidity were investigated by varying the {H2O} content and {HCl} concentration, respectively, in {MeCN/H2O} mixtures. For all compounds 1�-�7 investigated, intramolecular H abstraction by the nitro group from the exocyclic alpha-position with respect to the aryl moiety was found to be the primary process. The protolytic dissociation equilibrium of the resulting aci-nitro compound was kinetically characterized in the 0.1�-�10�mus time region. In general, two reaction channels compete for the aci-nitro compound and its anion: beta-elimination of the caged compound occurs from the anion, while from the undissociated aci-nitro compound, a nitrosobenzene derivative is formed with no release of the caged compound. The yield ratio of these two reaction channels can be controlled through shifts in the protolytic dissociation equilibrium of the aci-nitro compound. In solutions with either low basicity {(H2O-free} {MeCN)} or high acidity (higher concentration of {HCl} in {H2O/MeCN),} two as yet unidentified products are formed, each one specifically for one of the mentioned conditions.}, number = {6}, journal = {Helvetica Chimica Acta}, author = {Stefan Walbert and Wolfgang Pfleiderer and {Ulrich�E.} Steiner}, year = {2001}, pages = {1601--1611} }, @article{mahajan_oligonucleotide_2006, title = {Oligonucleotide Microarrays: Immobilization of Phosphorylated Oligonucleotides on Epoxylated Surface}, volume = {17}, url = {http://dx.doi.org/10.1021/bc0601065}, doi = {10.1021/bc0601065}, abstract = {A facile and efficient method for direct immobilization of phosphorylated oligonucleotides on an epoxy-activated glass surface is described. The new immobilization strategy has been analyzed for its performance in {DNA} microarray under both microwave and thermal conditions. It reflects high immobilization efficiency (23\%), and signal-to-noise ratio (98) and resulted in high hybridization efficiency (36\%) in comparison to those obtained with standard methods, viz., {NTMTA} (9.76\%) and epoxideamine (9.82\%). The probes immobilized through the new strategy were found to be heat-stable, since the performance of microarray decreased by only 7\% after subjecting it to 20 {PCR-like} heat cycles, suggesting that the chemistry could be used in integrated {PCR/microarray} devices. The immobilization of probes following the proposed chemistry resulted in spots of superior quality in terms of spot morphology, spot homogeneity, and signal reproducibility. The constructed microarrays have been successfully used for the discrimination of nucleotide mismatches. In conclusion, these features make the new immobilization strategy ideal for facile, efficient, and cost-effective manufacturing of {DNA} microarrays.}, number = {5}, journal = {Bioconjugate Chemistry}, author = {S. Mahajan and P. Kumar and K. C. Gupta}, year = {2006}, pages = {1184--1189} }, @article{shaginian_light-directed_2004, title = {{Light-Directed} Radial Combinatorial Chemistry: Orthogonal {Safety-Catch} Protecting Groups for the Synthesis of Small Molecule Microarrays}, volume = {126}, url = {http://dx.doi.org/10.1021/ja044702q}, doi = {10.1021/ja044702q}, abstract = {We describe the development of photolabile protecting groups based on the 3,4,5-trimethoxyphenacyl group {(TMP).} Orthogonal safety-catches were created by introducing an acid-activatible dimethyl ketal {(AA-TMP)} and an oxidatively activatible 1,3-dithiane {(OA-TMP)} into the photolabile {TMP} group. We demonstrate the application of these protecting groups in light-directed synthesis of small molecule microarrays with diversity elements radially attached to a hydroxyproline scaffold.}, number = {51}, journal = {Journal of the American Chemical Society}, author = {Alex Shaginian and Madhusudan Patel and {Mo-Huang} Li and Shane T. Flickinger and Changhan Kim and Franco Cerrina and Peter J. Belshaw}, month = dec, year = {2004}, pages = {16704--16705} }, @article{charbonnier_generic_2005, title = {A generic approach for the design of whole-genome oligoarrays, validated for genomotyping, deletion mapping and gene expression analysis on Staphylococcus aureus}, volume = {6}, issn = {1471-2164}, url = {http://www.biomedcentral.com/1471-2164/6/95}, doi = {10.1186/1471-2164-6-95}, abstract = {{BACKGROUND:DNA} microarray technology is widely used to determine the expression levels of thousands of genes in a single experiment, for a broad range of organisms. Optimal design of immobilized nucleic acids has a direct impact on the reliability of microarray results. However, despite small genome size and complexity, prokaryotic organisms are not frequently studied to validate selected bioinformatics approaches. Relying on parameters shown to affect the hybridization of nucleic acids, we designed freely available software and validated experimentally its performance on the bacterial pathogen Staphylococcus {aureus.RESULTS:We} describe an efficient procedure for selecting 40-60 mer oligonucleotide probes combining optimal thermodynamic properties with high target specificity, suitable for genomic studies of microbial species. The algorithm for filtering probes from extensive oligonucleotides libraries fitting standard thermodynamic criteria includes positional information of predicted target-probe binding regions. This algorithm efficiently selected probes recognizing homologous gene targets across three different sequenced genomes of Staphylococcus aureus. {BLAST} analysis of the final selection of 5,427 probes yielded {\textgreater}97\%, 93\%, and 81\% of Staphylococcus aureus genome coverage in strains N315, Mu50, and {COL,} respectively. A manufactured oligoarray including a subset of control Escherichia coli probes was validated for applications in the fields of comparative genomics and molecular epidemiology, mapping of deletion mutations and transcription {profiling.CONCLUSION:This} generic chip-design process merging sequence information from several related genomes improves genome coverage even in conserved regions.}, number = {1}, journal = {{BMC} Genomics}, author = {Yvan Charbonnier and Brian Gettler and Patrice Francois and Manuela Bento and Adriana Renzoni and Pierre Vaudaux and Werner Schlegel and Jacques Schrenzel}, year = {2005}, pages = {95} }, @article{wefers_analysis_1995, title = {Analysis of programmable ultrashort waveform generation using liquid-crystal spatial light modulators}, volume = {12}, url = {http://josab.osa.org/abstract.cfm?URI=josab-12-7-1343}, doi = {{10.1364/JOSAB.12.001343}}, abstract = {A rigorous analysis of ultrashort pulse shaping by the spectral filtering of dispersed frequency components is presented. Particular attention is directed toward the case of two liquid-crystal spatial light modulators used to provide programmable manipulation of both the phase and the amplitude profiles of the shaped waveform in the time domain. Different optical configurations are evaluated and their theoretical and practical effects determined. An important result is that, even with optimal alignment and components, the diffraction arising from spectral filtering necessarily produces a transverse spatial shift that varies linearly along the temporal profile of the shaped waveform. Despite this effect it is shown that the technique can generate arbitrary phase and amplitude temporal profiles (subject to limitations in temporal extent and temporal resolution) for the Gaussian spatial component of the shaped output waveform.}, number = {7}, journal = {Journal of the Optical Society of America B}, author = {Marc M. Wefers and Keith A. Nelson}, month = jul, year = {1995}, pages = {1343--1362} }, @misc{_viewmedia.pdf_????, title = {viewmedia.pdf}, url = {http://www.opticsinfobase.org/viewmedia.cfm?uri=ol-23-6-475&seq=0} }, @article{hebner_local_1998, title = {Local tuning of organic light-emitting diode color by dye droplet application}, volume = {73}, journal = {Applied Physics Letters}, author = {T. R. Hebner and J. C. Sturm}, year = {1998}, pages = {1775} }, @article{fatehi_optical_1981, title = {Optical logic gates using liquid crystal light valve: implementation and application example}, volume = {20}, url = {http://ao.osa.org/abstract.cfm?URI=ao-20-13-2250}, doi = {{10.1364/AO.20.002250}}, abstract = {In this paper, we propose a new method of optically implementing digital logic gates capable of performing all logic operations and give the technique for construction of an array of n-bit parallel adders as a typical application circuit. These gates are implemented using a Hughes liquid crystal light valve operated in the parallel off-state configuration. It is found that all possible functions of two binary variables are realizable with these gates, some as bright-true-logic and some as dark-true-logic. Experimental results will be given using the portions of a single liquid crystal light valve demonstrating the feasibility of {AND,} {NOR,} {XOR,} etc. gate arrays. As an example of implementation of combinatorial circuits, a design for an array of binary adders will also be given.}, number = {13}, journal = {Applied Optics}, author = {M. T. Fatehi and K. C. Wasmundt and Jr. Collins}, month = jul, year = {1981}, pages = {2250--2256} }, @article{cerrina_biological_2002, title = {Biological lithography: development of a maskless microarray synthesizer for {DNA} chips}, volume = {61-62}, issn = {0167-9317}, url = {http://www.sciencedirect.com/science/article/B6V0W-45CDHW7-1/2/3c4c7a0b836f91c1657eeb50e1117e3f}, doi = {{10.1016/S0167-9317(02)00566-X}}, abstract = { We have recently reported the development of a {DNA} maskless array synthesizer {(MAS)} {[Singh-Gasson} et al., Nat. Biotechnol. 17 (1999) 974]. In this paper we describe in more details the technical approach and implementation of the system, and show recent results of high-density {DNA} chips.}, journal = {Microelectronic Engineering}, author = {F. Cerrina and F. Blattner and W. Huang and Y. Hue and R. Green and S. {Singh-Gasson} and M. Sussman}, month = jul, year = {2002}, keywords = {{Biology,DNA} {array,Lithography,Micro} array}, pages = {33--40} }, @article{beattie_hybridization_1995, title = {Hybridization of {DNA} targets to glass-tethered oligonucleotide probes}, volume = {4}, url = {http://dx.doi.org/10.1007/BF02779015}, doi = {{10.1007/BF02779015}}, abstract = {Abstract Hybridization of nucleic acids to surface-tethered oligonucleotide probes has numerous potential applications in genome mapping and {DNA} sequence analysis. In this article, we describe a simple standard protocol for routine preparation of terminal amine-derivatized 9-mer oligonucleotide arrays on ordinary microscope slides and hybridization conditions with {DNA} target strands of up to several hundred bases in length with good discrimination against mismatches. Additional linker arms separating the glass surface from the probe sequence are not necessary. The technique described here offers a powerful tool for the detection of specific genetic mutations. }, number = {3}, journal = {Molecular Biotechnology}, author = {Wanda Beattie and Lin Meng and Saralinda Turner and Rajender Varma and Dat Dao and Kenneth Beattie}, month = dec, year = {1995}, pages = {213--225} }, @inbook{song_selectivity_2008, title = {Selectivity of Hybridization Controlled by the Density of Solid Phase Synthesized {DNA} Probes on Glass Substrates}, url = {http://dx.doi.org/10.1007/978-1-4020-6952-9_8}, abstract = {Optical biochip design based on varying the density of immobilized single-stranded {DNA} {(ssDNA)} oligonucleotide probes was examined. A method of immobilization was developed to yield various densities of probe molecules using photochemical activation of surfaces and in situ solid phase synthesis for {DNA} immobilization. High surface density of {ssDNA} probe (up to 1 × 1013 probes/cm2) was obtained using the immobilization method. The densities and extent of hybridization of nucleic acids were determined using confocal fluorescence microscopy. Selective hybridization of targets associated with spinal muscular atrophy containing single nucleotide polymorphisms {(SNP),} and their thermal denaturation profiles were investigated to examine the sensitivity and selectivity for {SNP} detection. The detection limit was less than 16 {pM} at room temperature. Single base mismatch discrimination was demonstrated based on control of melt temperature by selection of probe density, and temperature differences of {12-15°C} could be achieved for {SNP} determination. Importantly, the results demonstrate that poor control of probe density can result in significant variability of selectivity, as seen by melt temperature shifts of up to {5°C} in the density range that was investigated. }, booktitle = {Optical Waveguide Sensing and Imaging}, author = {Fayi Song and Ulrich J. Krull}, year = {2008}, pages = {195--210} }, @inproceedings{zuhong_lu_in_2002, title = {In situ synthesis of oligonucleotide arrays by using the molecular stamp method}, volume = {2}, isbn = {{1094-687X} }, doi = {{10.1109/IEMBS.2002.1106595}}, abstract = {This work developed a technique for in situ synthesis of oligonucleotide arrays on glass surfaces. In this method, based on the standard phosphoramidites chemistry protocol, the coupling was conducted through contacting glass surfaces with a set of molecular stamps on the surfaces of which nucleoside monomer and tetrazole mixed acetonitrile solution were spread. It was shown that 20-mer oligonucleotide on the glass slide was successfully synthesized using the modified polydimethylsiloxane stamps and showed high synthetic efficiency. An effective method has been used to eliminate residual reactive nucleosides on chip with small molecules containing a hydroxyl group. Specific oligonucleotide arrays of four probes including matches and mismatches with the target sequence were fabricated to identify the perfect match and mismatch sequences. Results indicated that the perfect match and mismatch probes hybridized fluorescent signals had clear differences, and may be used to identify and rapidly screen single-nucleotide polymorphisms.}, booktitle = {{[Engineering} in Medicine and Biology, 2002. 24th Annual Conference and the Annual Fall Meeting of the Biomedical Engineering Society] {EMBS/BMES} Conference, 2002. Proceedings of the Second Joint}, author = {Zuhong Lu and Pengfeng Xiao and Nongyue He and Zhengchun Liu and Quanguo He}, year = {2002}, keywords = {15 min,20-mer oligonucleotide,2 h,biochemistry,biological techniques,glass surfaces,high synthetic efficiency,hybridization fluorescent signals,hydroxyl group,in situ synthesis,macromolecules,match sequences,mismatch sequences,modified polydimethylsiloxane stamps,molecular biophysics,molecular stamp method,nucleoside monomer,oligonucleotide arrays,organic compounds,probes,residual reactive nucleosides elimination,standard phosphoramidites chemistry protocol,tetrazole mixed acetonitrile solution}, pages = {1671--1672 vol.2} }, @article{bader_oligonucleotide_1997, title = {Oligonucleotide Microsynthesis of A 200-mer and of {One-Dimensional} Arrays on a Surface Hydroxylated Polypropylene Tape}, volume = {16}, number = {5}, journal = {Nucleosides, Nucleotides and Nucleic Acids}, author = {R. Bader and M. Hinz and B. Schu and H. Seliger}, year = {1997}, pages = {829--833}, comment = {... The substitution of a polypropylene tape with hydroxyl groups for a derivatized glass support enables the synthesis of up to 200-mer oligonucleotides {(Bader} et ...} }, @article{tanaka_syringe_1982, title = {Syringe method for stepwise chemical synthesis of oligonucleotides}, volume = {10}, url = {http://nar.oxfordjournals.org/cgi/content/abstract/10/10/3249}, doi = {10.1093/nar/10.10.3249}, abstract = {A simple procedure is described for synthesis of oligonucleotides by phosphite chemistry. Chains can be constructed rapidly with minimal equipment (a syringe and reagent bottles). The method is illustrated by synthesis of {d-TGCAGGTT.} Pertinent supporting data on the effect of variations in the detritylation, condensation, oxidation, capping and cleavage steps in the synthetic approach and in isolation procedures are also presented. }, number = {10}, journal = {Nucl. Acids Res.}, author = {Toshiki Tanaka and Robert L. Letsinger}, month = may, year = {1982}, pages = {3249--3259} }, @article{goldmann_dna-printing:_2000, title = {{DNA-printing:} utilization of a standard inkjet printer for the transfer of nucleic acids to solid supports}, volume = {42}, issn = {{0165-022X}}, url = {http://www.sciencedirect.com/science/article/B6T28-3YKKB68-3/2/d9c4fc79821b16bb69902efde47c2328}, doi = {{10.1016/S0165-022X(99)00049-4}}, abstract = { The use of total {cDNA} as a probe for hybridization enables the transcription level of a large number of genes to be analyzed at the same time. Some effort has been spent to develop high density gene arrays on different solid supports to facilitate this hybridization. We achieved a high resolution by utilizing inkjet printer technology as a useful alternative to blotting the target genes onto a membrane. By the use of an ordinary inkjet printer model we show that it is possible to print {DNA} onto hybridization membranes and hybridize using either specific genes or total {cDNA} as probes. The high resolution of these prints (300 dpi) might be used in the future to construct complex micro-arrays to analyze simultaneously large numbers of genes.}, number = {3}, journal = {Journal of Biochemical and Biophysical Methods}, author = {Torsten Goldmann and Juan S. Gonzalez}, month = mar, year = {2000}, keywords = {{Blotting,Hybridization,Inkjet} {printer,Membranes,Nucleic} acids}, pages = {105--110} }, @article{chanteloup_nearly_1998, title = {Nearly diffraction-limited laser focal spot obtained by use of an optically addressed light valve in an adaptive-optics loop}, volume = {23}, url = {http://ol.osa.org/abstract.cfm?URI=ol-23-6-475}, doi = {{10.1364/OL.23.000475}}, abstract = {We demonstrate correction of laser wave-front distortions by use of an adaptive-optical technique based on a light valve. The setup consists of an achromatic and adjustable-sensitivity wave-front sensor and a wave-front corrector relying on an optically addressed liquid-crystal spatial light modulator. Experimental results with strongly aberrated beams focused close to the diffraction limit are presented for the cw regime. Additional experiments with pulses and measurement of damage thresholds show that this approach is relevant for spatial phase correction of ultraintense laser pulses.}, number = {6}, journal = {Optics Letters}, author = {{J.-C.} Chanteloup and H. Baldis and A. Migus and G. Mourou and B. Loiseaux and {J.-P.} Huignard}, month = mar, year = {1998}, keywords = {Active or adaptive {optics,Diffraction,Lasers} and laser optics}, pages = {475--477} }, @inbook{mcgall_photolithographic_2001, title = {Photolithographic Synthesis of {High-Density} Oligonucleotide Arrays}, url = {http://dx.doi.org/10.1385/1-59259-234-1:71}, booktitle = {{DNA} Arrays: Methods and Protocols}, author = {Glenn H. {McGall} and Jacqueline A. Fidanza}, year = {2001}, pages = {71--101} }, @article{sonoyama_ink-jet-printable_2008, title = {Ink-jet-printable phosphorescent organic light-emitting-diode devices}, volume = {16}, url = {http://link.aip.org/link/?JSI/16/1229/1}, doi = {{10.1889/JSID16.12.1229}}, number = {12}, journal = {Journal of the Society for Information Display}, author = {Takuya Sonoyama and Masaki Ito and Shunichi Seki and Satoru Miyashita and Sean Xia and Jason Brooks and {Kwang-Ohk} Cheon and Raymond C. Kwong and Michael Inbasekaran and Julie J. Brown}, month = dec, year = {2008}, pages = {1229--1236} }, @article{moddel_high-speed_????, title = {High-speed binary optically addressed spatial light modulator}, author = {G. Moddel and K. M. Johnson and W. Li and R. A. Rice and L. A. {Pagano-Stauffer} and M. A. Handschy} }, @article{zhou_microfluidic_2004, title = {Microfluidic {PicoArray} synthesis of oligodeoxynucleotides and simultaneous assembling of multiple {DNA} sequences}, volume = {32}, url = {http://nar.oxfordjournals.org/cgi/content/abstract/32/18/5409}, doi = {10.1093/nar/gkh879}, abstract = {Large {DNA} constructs of arbitrary sequences can currently be assembled with relative ease by joining short synthetic oligodeoxynucleotides (oligonucleotides). The ability to mass produce these synthetic genes readily will have a significant impact on research in biology and medicine. Presently, high-throughput gene synthesis is unlikely, due to the limits of oligonucleotide synthesis. We describe a microfluidic {PicoArray} method for the simultaneous synthesis and purification of oligonucleotides that are designed for multiplex gene synthesis. Given the demand for highly pure oligonucleotides in gene synthesis processes, we used a model to improve key reaction steps in {DNA} synthesis. The oligonucleotides obtained were successfully used in ligation under thermal cycling conditions to generate {DNA} constructs of several hundreds of base pairs. Protein expression using the gene thus synthesized was demonstrated. We used a {DNA} assembly strategy, i.e. ligation followed by fusion {PCR,} and achieved effective assembling of up to 10 kb {DNA} constructs. These results illustrate the potential of microfluidics-based ultra-fast oligonucleotide parallel synthesis as an enabling tool for modern synthetic biology applications, such as the construction of genome-scale molecular clones and cell-free large scale protein expression. }, number = {18}, journal = {Nucl. Acids Res.}, author = {Xiaochuan Zhou and Shiying Cai and Ailing Hong and Qimin You and Peilin Yu and Nijing Sheng and Onnop Srivannavit and Seema Muranjan and Jean Marie Rouillard and Yongmei Xia and Xiaolin Zhang and Qin Xiang and Renuka Ganesh and Qi Zhu and Anna Matejko and Erdogan Gulari and Xiaolian Gao}, month = oct, year = {2004}, pages = {5409--5417} }, @article{wattellier_beam-focus_2002, title = {Beam-focus shaping by use of programmable phase-only filters: application to an ultralong focal line}, volume = {27}, url = {http://ol.osa.org/abstract.cfm?URI=ol-27-4-213}, doi = {{10.1364/OL.27.000213}}, abstract = {We have developed a high-resolution programmable adaptive-optic device based on an optically addressed liquid-crystal electro-optic valve controlled by an achromatic three-wave lateral shearing interferometer. We apply this phase-only filter and loop to shape the far-field pattern of laser beams. As a first application, we theoretically compute and experimentally verify the focus along a line longer than tens of Rayleigh ranges.}, number = {4}, journal = {Optics Letters}, author = {B. Wattellier and C. Sauteret and {J.-C.} Chanteloup and A. Migus}, month = feb, year = {2002}, keywords = {Laser beam {shaping,Liquid} {crystals,Phase-only} filters }, pages = {213--215} }, @article{hebner_ink-jet_1998, title = {Ink-jet printing of doped polymers for organic light emitting devices}, volume = {72}, journal = {Applied Physics Letters}, author = {T. R. Hebner and C. C. Wu and D. Marcy and M. H. Lu and J. C. Sturm}, year = {1998}, pages = {519} }, @article{mcgall_efficiency_1997, title = {The Efficiency of {Light-Directed} Synthesis of {DNA} Arrays on Glass Substrates}, volume = {119}, url = {http://dx.doi.org/10.1021/ja964427a}, doi = {10.1021/ja964427a}, abstract = {New methods based on photolithography and surface fluorescence were used to determine photodeprotection rates and stepwise yields for light-directed oligonucleotide synthesis using photolabile {5`-(((alpha-methyl-2-nitropiperonyl)oxy)carbonyl)(MeNPOC)-2`-deoxynucleoside} phosphoramidites on planar glass substrates. Under {near-UV} illumination (primarily 365 nm) from a mercury light source, the rate of photoremoval of the {MeNPOC} protecting group was found to be independent of both the nucleotide and length of the growing oligomer (t1/2 = 12 s at 27.5 {mW/cm2).} A moderate dependence on solvent polarity was observed, with photolysis proceeding most rapidly in the presence of nonpolar solvents or in the absence of solvent (e.g., t1/2 = 1013 s at 27.5 {mW/cm2).} In solution, the photolysis rate was linearly dependent on light intensity over the range 550 {mW/cm2.} Average stepwise yields for the synthesis of dodecamer oligonucleotides were in the range of 9294\%, using monomers based on N6-(phenoxyacetyl)-2`-deoxyadenosine, N2-isobutyryl-2`-deoxyguanosine, N4-isobutyryl-2`-deoxycytidine, and thymidine. By comparison, an efficiency of 98\%/step was obtained using a conventional 5`-dimethoxytrityl monomer with acid deprotection on the same support. The lower yields associated with the photochemical process appears to be due to incomplete recovery of free 5`-hydroxyl groups after photolysis on the support, although high yields of {5`-OH} nucleosides (96\%) are consistently observed when {5`-MeNPOC} monomers are photolyzed in solution.}, number = {22}, journal = {Journal of the American Chemical Society}, author = {Glenn H. {McGall} and Anthony D. Barone and Martin Diggelmann and Stephen P. A. Fodor and Erik Gentalen and Nam Ngo}, month = jun, year = {1997}, pages = {5081--5090} }, @article{fisher_color_1983, title = {Color coded triarylmethyl protecting groups useful for deoxypolynucleotide synthesis}, volume = {11}, url = {http://nar.oxfordjournals.org/cgi/content/abstract/11/5/1589}, doi = {10.1093/nar/11.5.1589}, abstract = {Triarylmethyl groups having ditferent colors but similar chemical reactivities in acid were examined as potential aids for monitoring the stepwise addition of mononucleotides to a deoxy-oligonucleotide. The successful application of these protecting groups to deoxyoligonucleotide synthesis on polymer supports was demonstrated. }, number = {5}, journal = {Nucl. Acids Res.}, author = {{E.F.} Fisher and {M.H.} Caruthers}, month = mar, year = {1983}, pages = {1589--1599} }, @article{pierik_quality_2008, title = {Quality control of inkjet technology for {DNA} microarray fabrication}, volume = {3}, url = {http://dx.doi.org/10.1002/biot.200800121}, doi = {10.1002/biot.200800121}, abstract = {A robust manufacturing process is essential to make high-quality {DNA} microarrays, especially for use in diagnostic tests. We investigated different failure modes of the inkjet printing process used to manufacture low-density microarrays. A single nozzle inkjet spotter was provided with two optical imaging systems, monitoring in real time the flight path of every droplet. If a droplet emission failure is detected, the printing process is automatically stopped. We analyzed over 1.3 million droplets. This information was used to investigate the performance of the inkjet system and to obtain detailed insight into the frequency and causes of jetting failures. Of all the substrates investigated, 96.2\% were produced without any system or jetting failures. In 1.6\% of the substrates, droplet emission failed and was correctly identified. Appropriate measures could then be taken to get the process back on track. In 2.2\%, the imaging systems failed while droplet emission occurred correctly. In 0.1\% of the substrates, droplet emission failure that was not timely detected occurred. Thus, the overall yield of the microarray manufacturing process was 99.9\%, which is highly acceptable for prototyping.}, number = {12}, journal = {Biotechnology Journal}, author = {Anke Pierik and Frits Dijksman and Adrie Raaijmakers and Ton Wismans and Henk Stapert}, year = {2008}, pages = {1581--1590} }, @inproceedings{fox_reconfigurable_2007, address = {Monterey, {CA,} {USA}}, title = {Reconfigurable lithographic applications using polymer liquid crystal composite films}, volume = {6730}, url = {http://link.aip.org/link/?PSI/6730/673048/1}, booktitle = {Photomask Technology 2007}, publisher = {{SPIE}}, author = {Anna E. Fox and Adam K. Fontecchio and Robert J. Naber and Hiroichi Kawahira}, month = oct, year = {2007}, pages = {673048--10} }, @inproceedings{yong-sung_choi_hydrophilic_2006, title = {Hydrophilic and hydrophobic patterned template for {DNA} chip microarray}, volume = {1}, doi = {{10.1109/NMDC.2006.4388759}}, abstract = {Microarray-based {DNA} chips provide architecture for multi-analyte sensing. In this paper, we report a new approach for {DNA} chip microarray fabrication. Multifunctional {DNA} chip microarray was made by immobilizing many kinds of biomaterials on transducers (particles). {DNA} chip microarray was prepared by randomly distributing a mixture of the particles on a chip pattern containing thousands of mum-scale sites. The particles occupied a different sites from site to site. The particles were arranged on the chip pattern by the random fluidic self-assembly {(RFSA)} method, using a hydrophobic interaction for assembly.}, booktitle = {Nanotechnology Materials and Devices Conference, 2006. {NMDC} 2006. {IEEE}}, author = {{Yong-Sung} Choi and {Jong-Dae} Moon and {Young-Soo} Kwon and {Kyung-Sup} Lee}, year = {2006}, keywords = {biomaterials,biomolecular {electronics,DNA} chip microarray fabrication,hydrophili,hydrophilic patterned template,hydrophob,hydrophobic interaction,hydrophobic patterned template,integrated circuit manufacture,multi-analyte sensing,random fluidic,random fluidic self-assembly,template,transducers}, pages = {344--345} }, @article{beier_versatile_1999, title = {Versatile derivatisation of solid support media for covalent bonding on {DNA-microchips}}, volume = {27}, url = {http://nar.oxfordjournals.org/cgi/content/abstract/27/9/1970}, doi = {10.1093/nar/27.9.1970}, number = {9}, journal = {Nucl. Acids Res.}, author = {M Beier and {JD} Hoheisel}, month = may, year = {1999}, pages = {1970--1977} }, @article{rogers_immobilization_1999, title = {Immobilization of Oligonucleotides onto a Glass Support via Disulfide Bonds: A Method for Preparation of {DNA} Microarrays}, volume = {266}, issn = {0003-2697}, url = {http://www.sciencedirect.com/science/article/B6W9V-45HR75F-CY/2/a5524fee1b67980b44c204843aae5f2f}, doi = {10.1006/abio.1998.2857}, abstract = { The covalent attachment of disulfide-modified oligonucleotides to a mercaptosilane-modified glass surface is described. This method provides an efficient and specific covalent attachment chemistry for immobilization of {DNA} probes onto a solid support. Glass slides were derivatized with 3-mercaptopropyl silane for attachment of 5-prime disulfide-modified oligonucleotides via disulfide bonds. An attachment density of approximately 3 × 105oligonucleotides/[mu]m2was observed. Oligonucleotides attached by this method provided a highly efficient substrate for nucleic acid hybridization and primer extension assays. In addition, we have demonstrated patterning of multiple {DNA} probes on a glass surface utilizing this attachment chemistry, which allows for array densities of at least 20,000 spots/cm2.}, number = {1}, journal = {Analytical Biochemistry}, author = {{Yu-Hui} Rogers and Ping {Jiang-Baucom} and {Zhi-Jian} Huang and Valery Bogdanov and Stephen Anderson and Michael T. {Boyce-Jacino}}, year = {1999}, keywords = {covalent immobilization; oligonucleotide; glass; disulfide bonds; {DNA} microarray}, pages = {23--30} }, @article{marshall_do-it-yourself_????, title = {Do-it-yourself gene watching}, author = {E. Marshall} }, @article{xiao_dna_2001, title = {{DNA} microarray synthesis by using {PDMS} molecular stamp {(II)}}, volume = {44}, url = {http://dx.doi.org/10.1007/BF02879820}, doi = {{10.1007/BF02879820}}, abstract = {Abstract Based on the standard phosphoramidites chemistry protocol, two oligonucleotides synthetic routes were studied by contact stamping reactants to a modified glass slide. Route A was a contact coupling reaction, in which a nucleoside monomer was transferred and coupled to reactive groups {(OH)} on a substrate by spreading the nucleoside activated with tetrazole on a polydimethylsiloxane {(PDMS)} stamp. Route B was a contact detritylation, in which one nucleoside was fixed on the desired synthesis regions where dimethoxytrityl {(DMT)} protecting groups on the 5’-hydroxyl of the support-bound nucleoside were removed by stamping trichloroacetic acid {(TCA)} distributed on features on a {PDMS} stamp. Experiments showed that the synthetic yield and the reaction speed of route A were higher than those of route B. It was shown that 20 mer oligonucleotide arrays immobilized on the glass slide were successfully synthesized using the {PDMS} stamps, and the coupling efficiency showed no difference between the {PDMS} stamping and the conventional synthesis methods. }, number = {4}, journal = {Science in China Series B: Chemistry}, author = {Pengfeng Xiao and Nongyue He and Quanguo He and Chunxiu Zhang and Yiwen Wang and Zuhong Lu and Jiqing Xu}, year = {2001}, pages = {442--448} }, @misc{_pedot-tma_????, title = {{PEDOT-TMA} - Wikipedia, the free encyclopedia}, url = {http://en.wikipedia.org/wiki/PEDOT-TMA} }, @inbook{heller_use_2007, title = {Use of Electric Field Array Devices for Assisted Assembly of {DNA} Nanocomponents and Other Nanofabrication Applications}, url = {http://dx.doi.org/10.1007/978-0-387-25843-0_6}, abstract = {Microelectronic arrays utilizing electric field transport have been developed for {DNA} diagnostics (including infectious and genetic disease and cancer detection), for short tandem repeat {(STR)} forensics analysis, and for gene expression applications. In addition to these bioresearch and clinical diagnostic applications, such devices also have the potential to carry out the assisted assembly of a wide variety of molecular scale, nanoscale and microscale components into higher order structures. These microelectronic array devices are able to produce defined electric fields on their surfaces that allow molecules and other entities with high fidelity recognition properties to be transported to or from any site on the surface of the array. Such devices can utilize either {DC} electric fields which cause movement of entities by their relative charge, or {AC} electric fields which allow entities to be selectively positioned by their dielectric properties. An almost unlimited variety of molecules and nanocomponents can be utilized with these devices, including: {DNA,} {DNA} constructs with fluorescent, photonic or electronic transfer properties, {RNA,} {RNA} constructs, amino acids, peptides, proteins (antibodies, enzymes), nanoparticles (quantum dots, carbon nanotubes, nanowires), cells and even micron scale semiconductor components. Thus, electric field devices can be used for developing a unique highly parallel {“Pick} \& Place” fabrication process by which a variety of heterogeneous molecules, nanocomponents and micron sized objects with intrinsic self-assembly properties can be organized into higher order {2D} and {3D} structures and devices. The process represents a unique synergy of combining the best aspects of a “top-down” process with a “bottom-up” process. Finally, integration of optical tweezers for manipulation of live cells and microspheres in a similar microarray setup is demonstrated for the applications of biological delivery and invasive manipulation of these species. }, booktitle = {{BioMEMS} and Biomedical Nanotechnology}, author = {Michael J. Heller and Cengiz S. Ozkan and Mihrimah Ozkan}, year = {2007}, pages = {137--159} }, @article{hayashi_photolithography_2008, title = {Photolithography system with liquid crystal display as active gray-tone mask for {3D} structuring of photoresist}, volume = {144}, issn = {0924-4247}, url = {http://www.sciencedirect.com/science/article/B6THG-4S0PK6W-1/2/f0809b32b3c72f34fea1ed9ed57a5495}, doi = {10.1016/j.sna.2008.02.014}, abstract = { Layer manufacturing is generally utilized for the development of micro electromechanical systems {(MEMS)} and micro total analysis systems {([mu]TAS).} However, the preparation of multiple masks and repetitive exposure procedure prevents the rapid fabrication of {3D} microstructures. An active mask fabrication by using a liquid crystal display {(LCD)} as an electrically controllable photomask can simplify the layer manufacturing process. In addition, the gray-tone photolithography is available by using {LCD} lithography system, since the exposure distribution is easily controlled by an {LCD.} We have developed the {LCD} mask exposure system by using {UV} light source. Firstly, the patterning characteristics of the {UV} photoresist by exposing line and space patterns are evaluated, and then, a fundamental step shape is produced in order to verify the feasibility of gray-tone {UV} photolithography by using {LCD.} A shape with a different height can be fabricated without any repetitive exposure and development procedures. Finally, we confirmed the high patterning resolution such as 11 [mu]m using check patterns and fabricated {3D} step shapes by using the {LCD} as a gray-scale photomask.}, number = {2}, journal = {Sensors and Actuators A: Physical}, author = {Terutake Hayashi and Takayuki Shibata and Takahiro Kawashima and Eiji Makino and Takashi Mineta and Toru Masuzawa}, month = jun, year = {2008}, keywords = {Active {photomask,Gray-tone} {photolithography,Liquid} crystal {display,MEMS,[mu]TAS}}, pages = {381--388} }, @article{coleman_s-pixyl_1999, title = {The S-pixyl group: an efficient photocleavable protecting group for the 5' hydroxy function of deoxyribonucleosides}, volume = {40}, issn = {0040-4039}, url = {http://www.sciencedirect.com/science/article/B6THS-3XY2G81-1P/2/d9e19545d4734dc7b0b4f9649acef0a7}, doi = {{10.1016/S0040-4039(99)01563-4}}, abstract = { The 9-phenylthioxanthyl {(S-pixyl} or {S-Px)} group has been investigated as a photocleavable protecting group for primary alcohols, and specifically as a 5' hydroxy protecting group for deoxyribonucleosides. Several alcohols, including the four nucleosides with protected exocyclic amino functions, were protected in very good to excellent yield by treatment of 9-chloro-9-phenylthioxanthene 3 in dry pyridine to reveal the derivatized compounds. Irradiation of the protected substrates in neutral, aqueous solution regenerated the starting alcohols in excellent yield.}, number = {45}, journal = {Tetrahedron Letters}, author = {Michael P. Coleman and Mary K. Boyd}, month = nov, year = {1999}, keywords = {alcohols,nucleosides,photochemistry,protecting groups}, pages = {7911--7915} }, @article{chalmeau_self-aligned_2008-1, title = {Self-aligned patterns of multiple biomolecules printed in one step}, volume = {93}, url = {http://link.aip.org/link/?APL/93/133901/1}, doi = {10.1063/1.2990045}, number = {13}, journal = {Applied Physics Letters}, author = {J. Chalmeau and C. Thibault and F. Carcenac and C. Vieu}, year = {2008}, keywords = {atomic force microscopy,biological techniques,deformation,elastomers,molecular biophysics,nanobiotechnology}, pages = {133901--3} }, @inproceedings{shroff_fabrication_2001, address = {Washington, {DC} {(USA)}}, title = {Fabrication of parallel-plate nanomirror arrays for extreme ultraviolet maskless lithography}, volume = {19}, url = {http://link.aip.org/link/?JVB/19/2412/1}, doi = {10.1116/1.1417544}, booktitle = {The 45th international conference on electron, ion, and photon beam technology and nanofabrication}, publisher = {{AVS}}, author = {Yashesh Shroff and Yijian Chen and William Oldham}, month = nov, year = {2001}, keywords = {chemical interdiffusion,elemental semiconductors,germanium,micro-optics,mirrors,nanotechnology,optical arrays,optical design techniques,optical fabrication,scanning electron microscopy,silicon,ultraviolet lithography}, pages = {2412--2415} }, @article{kim_dna_2003, title = {{DNA} microarrays: An imaging study}, volume = {21}, url = {http://link.aip.org/link/?JVB/21/2946/1}, doi = {10.1116/1.1627802}, number = {6}, journal = {Journal of Vacuum Science \& Technology B: Microelectronics and Nanometer Structures}, author = {C. Kim and M. Li and A. Lowe and N. Venkataramaiah and K. Richmond and J. Kaysen and F. Cerrina}, month = nov, year = {2003}, keywords = {biomolecular {electronics,CCD} image sensors,photolithography}, pages = {2946--2950} }, @article{leimanis_microarray-based_2006, title = {A Microarray-based Detection System for Genetically Modified {(GM)} Food Ingredients}, volume = {61}, url = {http://dx.doi.org/10.1007/s11103-005-6173-4}, doi = {10.1007/s11103-005-6173-4}, abstract = {Abstract A multiplex {DNA} microarray chip was developed for simultaneous identification of nine genetically modified organisms {(GMOs),} five plant species and three {GMO} screening elements, i.e. the {35S} promoter, the nos terminator and the {nptII} gene. The chips also include several controls, such as that for the possible presence of {CaMV.} The on-chip detection was performed directly with {PCR} amplified products. Particular emphasis was placed on the reduction of the number of {PCR} reactions required and on the number of primers present per amplification tube. The targets were biotin labelled and the arrays were detected using a colorimetric methodology. Specificity was provided by specific capture probes designed for each {GMO} and for the common screening elements. The sensitivity of the assay was tested by experiments carried out in five different laboratories. The limit of detection was lower than 0.3\% {GMO} for all tests and in general around 0.1\% for most {GMOs.} The chip detection system complies with the requirements of current {EU} regulations and other countries where thresholds are established for the labelling of {GMO.} }, number = {1}, journal = {Plant Molecular Biology}, author = {Serge Leimanis and Marta Hernández and Sophie Fernández and Francine Boyer and Malcolm Burns and Shirin Bruderer and Thomas Glouden and Neil Harris and Othmar Kaeppeli and Patrick Philipp and Maria Pla and Pere Puigdomènech and Marc Vaitilingom and Yves Bertheau and José Remacle}, month = may, year = {2006}, pages = {123--139} }, @article{tolonen_optimized_2002, title = {Optimized in situ construction of oligomers on an array surface}, volume = {30}, url = {http://nar.oxfordjournals.org/cgi/content/abstract/30/20/e107}, doi = {10.1093/nar/gnf106}, abstract = {Oligonucleotide arrays are powerful tools to study changes in gene expression for whole genomes. These arrays can be synthesized by adapting photolithographic techniques used in microelectronics. Using this method, oligonucleotides are built base by base directly on the array surface by numerous cycles of photodeprotection and nucleotide addition. In this paper we examine strategies to reduce the number of synthesis cycles required to construct oligonucleotide arrays. By computer modeling oligonucleotide synthesis, we found that the number of required synthesis cycles could be significantly reduced by focusing upon how oligonucleotides are chosen from within genes and upon the order in which nucleotides are deposited on the array. The methods described here could provide a more efficient strategy to produce oligonucleotide arrays. }, number = {20}, journal = {Nucl. Acids Res.}, author = {Andrew C. Tolonen and Dinu F. Albeanu and Julia F. Corbett and Heather Handley and Charlotte Henson and Pratap Malik}, month = oct, year = {2002}, pages = {e107} }, @article{gao_flexible_2001, title = {A flexible light-directed {DNA} chip synthesis gated by deprotection using solution photogenerated acids}, volume = {29}, url = {http://nar.oxfordjournals.org/cgi/content/abstract/29/22/4744}, doi = {10.1093/nar/29.22.4744}, abstract = {Oligonucleotide microarrays or {oDNA} chips are effective decoding and analytical tools for genomic sequences and are useful for a broad range of applications. Therefore, it is desirable to have synthesis methods of {DNA} chips that are highly flexible in sequence design and provide high quality and general adoptability. We report herein, {DNA} microarray synthesis based on a flexible biochip method. Our method simply uses photogenerated acid {(PGA)} in solution to trigger deprotection of the {5'-OH} group in conventional nucleotide phosphoramidite monomers (i.e. {PGA-gated} deprotection), with the rest of the reactions in the synthesis cycle the same as those used for routine synthesis of oligonucleotides. The complete {DNA} chip synthesis process is accomplished on a regular {DNA} synthesizer that is coupled with a {UV-VIS} projection display unit for performing digital photolithography. Using this method, {oDNA} chips containing probes of newly discovered genes can be quickly and easily synthesized at high yields in a conventional laboratory setting. Furthermore, the {PGA-gated} chemistry should be applicable to microarray syntheses of a variety of combinatorial molecules, such as peptides and organic molecules. }, number = {22}, journal = {Nucl. Acids Res.}, author = {Xiaolian Gao and Eric {LeProust} and Hua Zhang and Onnop Srivannavit and Erdogan Gulari and Peilin Yu and Ciro Nishiguchi and Qin Xiang and Xiaochuan Zhou}, month = nov, year = {2001}, pages = {4744--4750} }, @article{chang_dual-color_1998, title = {Dual-color polymer light-emitting pixels processed by hybrid inkjet printing}, volume = {73}, journal = {Applied Physics Letters}, author = {S. C. Chang and J. Bharathan and Y. Yang and R. Helgeson and F. Wudl and M. B. Ramey and J. R. Reynolds}, year = {1998}, pages = {2561} }, @article{golden_do-it-yourself_2005, title = {A "do-it-yourself" array biosensor}, volume = {37}, issn = {1046-2023}, url = {http://www.sciencedirect.com/science/article/B6WN5-4H7T0P9-1/2/f09f0cd45dcaa4774170bbc1c5404636}, doi = {10.1016/j.ymeth.2005.05.010}, abstract = { We have developed an array biosensor for the simultaneous detection of multiple targets in multiple samples within 15-30 min. The biosensor is based on a planar waveguide, a modified microscope slide, with a pattern of small (mm2) sensing regions. The waveguide is illuminated by launching the emission of a 635 nm diode laser into the proximal end of the slide via a line generator. The evanescent field excites fluorophores bound in the sensing region and the emitted fluorescence is measured using a Peltier-cooled {CCD} camera. Assays can be performed on the waveguide in multichannel flow chambers and then interrogated using the detection system described here. This biosensor can detect many different targets, including proteins, toxins, cells, virus, and explosives with detection limits rivaling those of the {ELISA} detection system.}, number = {1}, journal = {Methods}, author = {Joel Golden and Lisa {Shriver-Lake} and Kim Sapsford and Frances Ligler}, month = sep, year = {2005}, keywords = {{Array,Biosensor,Evanescent} {wave,Fluorescence,Planar} waveguide}, pages = {65--72} }, @article{xiao_in_2002, title = {In situ synthesis of oligonucleotide arrays by using soft lithography}, volume = {13}, number = {6}, journal = {Nanotechnology}, author = {P. F. Xiao and N. Y. He and Z. C. Liu and Q. G. He and X. Sun and Z. H. Lu}, year = {2002}, pages = {756--762} }, @inproceedings{mcgall_high-density_2000, address = {San Jose, {CA,} {USA}}, title = {High-density oligonucleotide probe arrays}, volume = {3926}, url = {http://link.aip.org/link/?PSI/3926/106/1}, booktitle = {Advances in Nucleic Acid and Protein Analyses, Manipulation, and Sequencing}, publisher = {{SPIE}}, author = {Glenn H. {McGall} and Jacqueline A. Fidenza and Patrick A. Limbach and John C. Owicki and Ramesh Raghavachari and Weihong Tan}, month = mar, year = {2000}, pages = {106--110} }, @inproceedings{xiao_fabrication_2001, address = {Nanjing, China}, title = {Fabrication of microstamps used for oligonucleotide array synthesis}, volume = {4601}, url = {http://link.aip.org/link/?PSI/4601/401/1}, booktitle = {Micromachining and Microfabrication Process Technology and Devices}, publisher = {{SPIE}}, author = {Pengfeng Xiao and Nongyao He and Zhengchun Liu and Quanguo He and Jiqing Xu and Zuhong Lu and Norman C. Tien and {Qing-An} Huang}, month = oct, year = {2001}, pages = {401--405} }, @article{hughes_expression_2001, title = {Expression profiling using microarrays fabricated by an ink-jet oligonucleotide synthesizer}, volume = {19}, issn = {1087-0156}, url = {http://dx.doi.org/10.1038/86730}, doi = {10.1038/86730}, number = {4}, journal = {Nat Biotech}, author = {Timothy R. Hughes and Mao Mao and Allan R. Jones and Julja Burchard and Matthew J. Marton and Karen W. Shannon and Steven M. Lefkowitz and Michael Ziman and Janell M. Schelter and Michael R. Meyer and Sumire Kobayashi and Colleen Davis and Hongyue Dai and Yudong D. He and Sergey B. Stephaniants and Guy Cavet and Wynn L. Walker and Anne West and Ernest Coffey and Daniel D. Shoemaker and Roland Stoughton and Alan P. Blanchard and Stephen H. Friend and Peter S. Linsley}, month = apr, year = {2001}, pages = {342--347} }, @article{beier_synthesis_2001, title = {Synthesis of Photolabile {5prime-{\textless}I{\textgreater}O{\textless}/I{\textgreater}-Phosphoramidites} for the Photolithographic Production of Microarrays of Inversely Oriented Oligonucleotides}, volume = {84}, url = {http://dx.doi.org/10.1002/1522-2675(20010711)84:7<2089::AID-HLCA2089>3.0.CO;2-0}, doi = {{10.1002/1522-2675(20010711)84:7{\textless}2089::AID-HLCA2089{\textgreater}3.0.CO;2-0}}, abstract = {The photolabile {3prime-O-{[2-(2-nitrophenyl)propoxy]carbonyl}-protected} 5prime-phosphoramidites (16�-�18) were synthesized (see Scheme) for an alternative mode of light-directed production of oligonucleotide arrays. Because of the characteristics of these monomeric building blocks, photolithographic in situ {DNA} synthesis occurred in 5primerarr3prime direction, in agreement with the orientation of enzymatic synthesis. Synthesis yields were as good as those of conventional reactions. The resulting oligonucleotides are attached to the surface via their 5prime-termini, while the 3prime-hydroxy groups are available as substrates for enzymatic reactions such as primer extension upon hybridization of a {DNA} template (see Fig.�2). The production of such oligonucleotide chips adds new procedural avenues to the growing number of applications of {DNA} microarrays.}, number = {7}, journal = {Helvetica Chimica Acta}, author = {Markus Beier and Achim Stephan and {J�rg�D.} Hoheisel}, year = {2001}, pages = {2089--2095} }, @article{rouillard_oligoarray_2003, title = {{OligoArray} 2.0: design of oligonucleotide probes for {DNA} microarrays using a thermodynamic approach}, volume = {31}, url = {http://nar.oxfordjournals.org/cgi/content/abstract/31/12/3057}, doi = {10.1093/nar/gkg426}, abstract = {There is a substantial interest in implementing bioinformatics technologies that allow the design of oligonucleotides to support the development of microarrays made from short synthetic {DNA} fragments spotted or in situ synthesized on slides. Ideally, such oligonucleotides should be totally specific to their respective targets to avoid any cross-hybridization and should not form stable secondary structures that may interfere with the labeled probes during hybridization. We have developed {OligoArray} 2.0, a program that designs specific oligonucleotides at the genomic scale. It uses a thermodynamic approach to predict secondary structures and to calculate the specificity of targets on chips for a unique probe in a mixture of labeled probes. Furthermore, {OligoArray} 2.0 can adjust the oligonucleotide length, according to user input, to fit a narrow Tm range compatible with hybridization requirements. Combined with on chip oligonucleotide synthesis, this program makes it feasible to perform expression analysis on a genomic scale for any organism for which the genome sequence is known. This is without relying on {cDNA} or oligonucleotide libraries. {OligoArray} 2.0 was used to design 75 764 oligonucleotides representing 26 140 transcripts from Arabidopsis thaliana. Among this set, we provide at least one specific oligonucleotide for 93\% of these transcripts. }, number = {12}, journal = {Nucl. Acids Res.}, author = {{Jean-Marie} Rouillard and Michael Zuker and Erdogan Gulari}, month = jun, year = {2003}, pages = {3057--3062} }, @article{kessels_versatile_2007, title = {Versatile stepper based maskless microlithography using a liquid crystal display for direct write of binary and multilevel microstructures}, volume = {6}, url = {http://link.aip.org/link/?JMM/6/033002/1}, number = {3}, journal = {Journal of {Micro/Nanolithography,} {MEMS} and {MOEMS}}, author = {Melanie V. Kessels and Marwa El Bouz and Robin Pagan and Kevin Heggarty}, month = jul, year = {2007}, keywords = {liquid crystal displays,microdisplays,micromechanical devices,photoresists,plotters}, pages = {033002--12} }, @article{fox_lineshape_2008, title = {Lineshape and morphology study of structures formed using a reconfigurable photomasking element}, volume = {7}, url = {http://link.aip.org/link/?JMM/7/033007/1}, number = {3}, journal = {Journal of {Micro/Nanolithography,} {MEMS} and {MOEMS}}, author = {Anna E. Fox and Adam K. Fontecchio}, month = jul, year = {2008}, keywords = {holographic gratings,liquid crystals,masks,optical films,organic compounds,photoresists,polymer dispersed liquid crystals,surface morphology}, pages = {033007--6} }, @article{blanchard_high-density_1996, title = {High-density oligonucleotide arrays}, volume = {11}, issn = {0956-5663}, url = {http://www.sciencedirect.com/science/article/B6TFC-3TKNNYK-D/2/6cacdf0323003bfff450b4658a86025a}, doi = {10.1016/0956-5663(96)83302-1}, abstract = { We are attempting to produce high-density arrays of surface-bound oligonucleotides for hybridization experiments. Our approach is to mechanically miniaturize conventional {DNA} synthesis chemistry. Ink-jet printer heads are used to deliver small drops of reagents to a chemically modified silicon dioxide surface, where they react to synthesize {DNA.} The drops are confined to small areas by a pattern of hydrophobic surface modifications, thus allowing the formation of high-density arrays without mixing between adjacent drops.}, number = {6-7}, journal = {Biosensors and Bioelectronics}, author = {A. P. Blanchard and R. J. Kaiser and L. E. Hood}, year = {1996}, keywords = {{DNA} hybridization,ink-jet,oligonucleotides arrays}, pages = {687--690} }, @article{taylor_impact_2003, title = {Impact of surface chemistry and blocking strategies on {DNA} microarrays}, volume = {31}, url = {http://nar.oxfordjournals.org/cgi/content/abstract/31/16/e87}, doi = {10.1093/nar/gng086}, abstract = {The surfaces and immobilization chemistries of {DNA} microarrays are the foundation for high quality gene expression data. Four surface modification chemistries, {poly-L-lysine} {(PLL),} 3-glycidoxypropyltrimethoxysilane {(GPS),} {DAB-AM-poly(propyleminime} hexadecaamine) dendrimer {(DAB)} and 3-aminopropyltrimethoxysilane {(APS),} were evaluated using {cDNA} and oligonucleotide sub-arrays. Two un-silanized glass surfaces, {RCA-cleaned} and immersed in {Tris-EDTA} buffer were also studied. {DNA} on amine-modified surfaces was fixed by {UV} (90 {mJ/cm2),} while {DNA} on {GPS-modified} surfaces was immobilized by covalent coupling. Arrays were blocked with either succinic anhydride {(SA),} bovine serum albumin {(BSA)} or left unblocked prior to hybridization with labeled {PCR} product. Quality factors evaluated were surface affinity for {cDNA} versus oligonucleotides, spot and background intensity, spotting concentration and blocking chemistry. Contact angle measurements and atomic force microscopy were preformed to characterize surface wettability and morphology. The {GPS} surface exhibited the lowest background intensity regardless of blocking method. Blocking the arrays did not affect raw spot intensity, but affected background intensity on amine surfaces, {BSA} blocking being the lowest. Oligonucleotides and {cDNA} on unblocked {GPS-modified} slides gave the best signal (spot-to-background intensity ratio). Under the conditions evaluated, the unblocked {GPS} surface along with amine covalent coupling was the most appropriate for both {cDNA} and oligonucleotide microarrays. }, number = {16}, journal = {Nucl. Acids Res.}, author = {Scott Taylor and Stephanie Smith and Brad Windle and Anthony {Guiseppi-Elie}}, month = aug, year = {2003}, pages = {e87} }, @article{woell_more_2004, title = {More Efficient Photolithographic Synthesis of {DNA-Chips} by Photosensitization}, volume = {35}, url = {http://dx.doi.org/10.1002/chin.200407256}, doi = {10.1002/chin.200407256}, abstract = {For Abstract see {ChemInform} Abstract in Full Text.}, number = {7}, journal = {{ChemInform}}, author = {D. Woell and S. Walbert and {K.-P.} Stengele and R. Green and T. Albert and W. Pfleiderer and U. E. Steiner}, year = {2004} }, @article{berroy_photolabile_2001, title = {Photolabile group for {5'-OH} protection of nucleosides: synthesis and photodeprotection rate}, volume = {74}, issn = {0925-4005}, url = {http://www.sciencedirect.com/science/article/B6THH-42RVRBK-10/2/f8bd8895d5945d824d8907cbd9a3440b}, doi = {{10.1016/S0925-4005(00)00731-0}}, abstract = { In this paper, we described the properties of a new photolabile group, 2-(3,4-methylenedioxy-6-nitrophenyl)propoxycarbonyl, {MNPPOC.} In spite of moderate yields of synthesis, photolytic properties could be analyzed for {5'-OH} protected T and {dAiBu.} The half-lives (t1/2) 11 and 12 s were found, respectively, with a good recovery of the corresponding deprotected deoxynucleoside (95-99\%). The photolysis rate of this new photolabile group was five-fold faster than the {MeNPOC} one.}, number = {1-3}, journal = {Sensors and Actuators B: Chemical}, author = {P. Berroy and M. L. Viriot and M. C. Carré}, month = apr, year = {2001}, keywords = {{DNA} {array,Photolabile} {groups,Photolysis,Protection} of deoxynucleosides}, pages = {186--189} }, @inproceedings{maier_impact_????, title = {Impact of microdrops on solid surfaces for {DNA-synthesis}}, author = {C. Maier and S. aus der Wiesche and E. P. Hofer} }, @article{igasaki_high_1999, title = {High Efficiency {Electrically-Addressable} {Phase-Only} Spatial Light Modulator}, volume = {6}, url = {http://dx.doi.org/10.1007/s10043-999-0339-2}, doi = {10.1007/s10043-999-0339-2}, abstract = {To realize a high efficiency electrically addressable phase-only modulator, we have coupled a liquid crystal display {(LCD)} to an optically addressed parallel-aligned nematic liquid crystal spatial light modulator {(PAL-SLM)} with a set of lenses. Phase modulation exceeding 3ϖ at 532 nm wavelength was obtained. We obtained linear transfer characteristics for phase modulation at various desired phase levels after calibration and adjustment of the transfer characteristics of the {PAL-SLM} and the {LCD.} Diffraction efficiency of 40\% for binary phase grating and of 90\% for 8-level blazed phase grating, which were very close to the simulation values, were observed. The power loss of the readout light was caused when passed through a half mirror, therefore, we examined a setup using an oblique readout light at the modulator. Very high diffraction efficiency was obtained from the setup by optimizing the polarization direction and optical path for this light, and the orientation of liquid crystals. Since the modulator can perform at better than 90\% diffraction efficiency and at nearly 100\% reflectivity, various high efficiency systems utilizing such modulators are expected.}, number = {4}, journal = {Optical Review}, author = {Yasunori Igasaki and Fanghong Li and Narihiro Yoshida and Haruyoshi Toyoda and Takashi Inoue and Naohisa Mukohzaka and Yuji Kobayashi and Tsutomu Hara}, month = jul, year = {1999}, pages = {339--344} }, @article{merrin_printing_2007, title = {Printing Multistrain Bacterial Patterns with a Piezoelectric Inkjet Printer}, volume = {2}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1914381}, doi = {10.1371/journal.pone.0000663}, number = {7}, journal = {{PLoS} {ONE}}, author = {Jack Merrin and Stanislas Leibler and John S. Chuang}, year = {2007}, note = {{PMC1914381}}, pages = {e663} }, @article{potyrailo_multi-wavelength_2009, title = {Multi-wavelength operation of optical disk drives for chemical and biological analysis}, volume = {136}, issn = {0925-4005}, url = {http://www.sciencedirect.com/science/article/B6THH-4V2NKBJ-1/2/3a0e44e0b4ae3e29b5415613a425d431}, doi = {10.1016/j.snb.2008.10.071}, abstract = { Optical disk drives have lasers that operate at 405, 650, and 780 nm making these devices attractive for a wide variety of analytical applications. Here we demonstrate the use of super audio compact disks {(SACDs)} and computer optical disk drives for multi-wavelength chemical measurements. As an example, dual-chemistry chlorine sensing films were formulated using combinatorial techniques and deposited onto {SACDs.} The chlorine response was measured at the analytical wavelength (780 nm), while thickness variations were normalized using the response at the 650-nm reference wavelength where the sensing films were not affected by chlorine exposure. Compared to a single-wavelength readout, this dual-wavelength approach improved the linear correlation coefficient {(R2)} from 0.76 to 0.95 and the limit of analyte detection from 600 to 300 ppb. The use of multi-wavelength optical disk drives should enable chemical and biological sensing with the expanded diversity of sensing chemistries and the advantages of multi-wavelength spectral processing.}, number = {1}, journal = {Sensors and Actuators B: Chemical}, author = {Radislav A. Potyrailo and William G. Morris and Ronald Wroczynski and Lamyaa Hassib and Peter Miller and Benjamin Dworken and Andrew M. Leach and Scott Boyette and Caibin Xiao}, month = feb, year = {2009}, keywords = {{DVD,Lab-on-disk,Optical} {disk,Optical} disk {drive,Optical} sensor {film,Super} audio {CD}}, pages = {203--208} }, @article{damha_improved_1990, title = {An improved procedure for derivatization of controlled-pore glass beads for solid-phase oligonucleotide synthesis}, volume = {18}, url = {http://nar.oxfordjournals.org/cgi/content/abstract/18/13/3813}, doi = {10.1093/nar/18.13.3813}, abstract = {A simplified and economical method for the attachment of 2'-deoxyribo, ribo and arabinonucleosides onto long-chain alkylamidopropanoic acid controlled-pore glass {(LCAAP-CPG,} P-3) is described. In this procedure, 5'-0-tritylated nucleosides are coupled directly to {LCAAP-CPG} in excellent yields using 1-(3-dimethylamino-propyl)-3-ethylcarbodiimide {(DEC)} as coupling reagent. The conventional and time-consuming preparation of {nucleoside-3'-O-succinates} is no longer required. }, number = {13}, journal = {Nucl. Acids Res.}, author = {Masad J. Damha and Paul A. Giannaris and Steven V. Zabarylo}, month = jul, year = {1990}, pages = {3813--3821} }, @article{larson_controlled_2004, title = {Controlled deposition of picoliter amounts of fluid using an ultrasonically driven micropipette}, volume = {75}, url = {http://link.aip.org/link/?RSI/75/832/1}, doi = {10.1063/1.1688436}, number = {4}, journal = {Review of Scientific Instruments}, author = {Bradley J. Larson and Susan D. Gillmor and Max G. Lagally}, month = apr, year = {2004}, keywords = {lead compounds,liquid phase deposition,molecular biophysics,piezoelectric materials,plotters,ultrasonic applications,zirconium compounds}, pages = {832--836} }, @article{fox_liquid_2007, title = {Liquid crystal polymer composite films for reconfigurable photomasking applications}, volume = {91}, url = {http://link.aip.org/link/?APL/91/141119/1}, doi = {10.1063/1.2794735}, number = {14}, journal = {Applied Physics Letters}, author = {Anna E. Fox and Adam K. Fontecchio}, month = oct, year = {2007}, keywords = {electrodes,holographic gratings,liquid films,masks,optical polymers,photoresists,polymer dispersed liquid crystals,polymer films}, pages = {141119--3} }, @article{pless_solid_1975, title = {Solid support synthesis of ollgothymidylates using phosphorochloridates and 1-alkylimidazoles}, volume = {2}, url = {http://nar.oxfordjournals.org/cgi/content/abstract/2/6/773}, doi = {10.1093/nar/2.6.773}, abstract = {A study of the synthesis of oligothymidylates via phosphotriester intermediates on a polystyrene support is described. The sequence involves condensation of a phenyl nucleoside-3'-phosphorochloridate with the 5'-hydroxyl group of the carrier bound oligonucleotide derivative in the presence of 1-methylimidazole. Conditions for preparation of the phenyl nucleoside phosphorochloridate as well as for the condensation on the support are discussed. {d-TpTpTpT} was obtained in 31\% overall yield from carrier bound thymidine in one series of experiments, and {d-TpTpTpTpT} was obtained in 9\% yield in another. The cycle for addition of one nucleotide unit can be completed in about six hours. }, number = {6}, journal = {Nucl. Acids Res.}, author = {Reynaldo C. Pless and Robert L. Letsinger}, month = jun, year = {1975}, pages = {773--786} }, @inproceedings{kim_biological_2004, address = {San Diego, California {(USA)}}, title = {Biological lithography: Improvements in {DNA} synthesis methods}, volume = {22}, url = {http://link.aip.org/link/?JVB/22/3163/1}, doi = {10.1116/1.1824066}, booktitle = {The 48th International Conference on Electron, Ion, and Photon Beam Technology and Nanofabrication}, publisher = {{AVS}}, author = {C. Kim and M. Li and M. Rodesch and A. Lowe and K. Richmond and F. Cerrina}, month = nov, year = {2004}, keywords = {biological techniques,biomolecular electronics,light scattering,masks,molecular {biophysics,Monte} Carlo methods,photolithography,physiological models}, pages = {3163--3167} }, @article{tokito_high-efficiency_2003, title = {High-efficiency phosphorescent polymer light-emitting devices}, volume = {4}, issn = {1566-1199}, url = {http://www.sciencedirect.com/science/article/B6W6J-49G6RD7-4/2/d1fe292eba07f3dcb56dbdf1032451f6}, doi = {10.1016/j.orgel.2003.08.005}, abstract = { In this paper, we describe the performance of polymer light-emitting devices {(PLEDs)} that are based on phosphorescent polymers involving a carbazole unit and an iridium-complex unit. The {PLEDs} exhibit red, green or blue emission, depending on the phosphorescent polymer used in the emissive layer. We achieved highly external quantum efficiencies of 5.5\%, 9\% and 3.5\% in respective red, green and blue {PLEDs} by selecting the electron transport material for the emissive layer and optimizing the content of the iridium-complex unit in the phosphorescent polymer chain. Furthermore, we demonstrated white emission in {PLEDs} by using blue-phosphorescent and red-phosphorescent polymers. An external quantum efficiency of 4.5\% was obtained for this emission.}, number = {2-3}, journal = {Organic Electronics}, author = {Shizuo Tokito and Mitsunori Suzuki and Fumio Sato and Motoaki Kamachi and Kourou Shirane}, month = sep, year = {2003}, pages = {105--111} }, @article{wll_triplet-sensitized_2004, title = {{Triplet-Sensitized} Photodeprotection of Oligonucleotides in Solution and on Microarray Chips}, volume = {87}, url = {http://dx.doi.org/10.1002/hlca.200490015}, doi = {10.1002/hlca.200490015}, abstract = {Conditions and kinetics of triplet sensitization as a method for increasing the light sensitivity of photolabile protecting groups used for the photolithographic synthesis of oligonucleotide microarrays were quantitatively studied with the photolabile 2-(2-nitrophenyl)propyl protecting group in homogeneous solutions and on glass substrates by using laser flash photolysis, continuous illumination with {HPLC} analysis, fluorescence dye labelling, and hybridization. In terms of efficiency and avoidance of chemical side reactions, {9H-thioxanthen-9-one} was the most-suitable sensitizer. Both in solution and on a glass substrate, the photostationary kinetics were quantitatively modelled and the relevant kinetic parameters determined. While the sensitization kinetics was diffusion-controlled both in solution and on the chip, the photostationary kinetics was essentially of zero order only on the chip because here the triplet-quenching effect of the released photoproduct 2-(2-nitrophenyl)propene was suppressed as a consequence of the inhomogeneous reaction that took place in a narrow diffusion zone above the surface from where the photoproducts could quickly escape. The kinetic simulation allowed quantitative estimate of the density of reactive groups on the surface. It was further demonstrated that, with {9H-thioxanthen-9-one} as a sensitizer, high-density oligonucleotide microarrays of high quality can be produced with one-third of the normal exposure time.}, number = {1}, journal = {Helvetica Chimica Acta}, author = {Dominik W�ll and Stefan Walbert and {Klaus-Peter} Stengele and {Tom�J.} Albert and Todd Richmond and Jason Norton and Michael Singer and {Roland�D.} Green and Wolfgang Pfleiderer and {Ulrich�E.} Steiner}, year = {2004}, pages = {28--45} }, @article{smith_proposal_1996, title = {A proposal for maskless, zone-plate-array nanolithography}, volume = {14}, number = {6}, journal = {Journal of Vacuum Science and {Technology-Section} {B-Microelectronics} Nanometer Structur}, author = {H. I. Smith}, year = {1996}, pages = {4318--4322} }, @inbook{rampal_construction_2007, title = {Construction of In Situ Oligonucleotide Arrays on Plastic}, url = {http://dx.doi.org/10.1007/978-1-59745-303-5_11}, booktitle = {Microarrays}, author = {Jang B. Rampal and Peter J. Coassin and Robert S. Matson}, year = {2007}, pages = {227--246} }, @misc{_ink-jet-printable_????-1, title = {Ink-jet-printable phosphorescent organic light-emitting-diode devices}, url = {http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normal&id=JSIDE8000016000012001229000001&idtype=cvips&gifs=yes} }