+# more notes

+

+* DNA polymerase

+* RNA polymerase

+* DNA-dependent DNA polymerase

+* RNA-dependent DNA polymerase

+* DNA-dependent RNA polymerase

+* RNA-dependent RNA polymerase

+* telomerase

+* reverse transcriptase (RNA-dependent DNA polymerase)

+* nucleotidyl transferase <https://www.nlm.nih.gov/cgi/mesh/2011/MB_cgi?mode=&term=Nucleotidyltransferases>

+

+

+DNA-directed vs DNA-dependent ??

+

+

+* Polyribonucleotide Nucleotidyltransferase (PNPASE) <https://en.wikipedia.org/wiki/Polynucleotide_phosphorylase>

+* DNA-directed DNA polymerase

+

+

+* DNA nucleotidylexotransferase (same as terminal deoxynucleotidyl transferase ??)

+

+* templateless polymerases if any

+

+

+# also check

+

+* recombinase

+* CRISPR stuff

+* helicase

+* replicase

+* DNA ligase

+* RNA ligase

+* RNA ligase ribozyme

+* RNA helicase

+* RNA replicase

+*

+

+

+terminal deoxynucleotide transferase

+

+terminal deoxyribonucleotidyltransferase

+terminal transferase

+TdT

+addase activity

+

+

+<https://en.wikipedia.org/wiki/Terminal_deoxynucleotidyl_transferase>

+

+

+

+* telomerase reverse transcriptase (TERT) <https://en.wikipedia.org/wiki/Telomerase_reverse_transcriptase>

+** has an RNA component that encodes the template for addition

+

+# Large components

+

+* Siderophore biosynthesis non-ribosomal peptide synthetase module <http://www.uniprot.org/uniprot/A0A108U5E5>

+

+* Polymerase/replicase <http://www.uniprot.org/uniprot/J7I0T0> -- RNA-directed RNA polymerase activity, RdRp catalytic peptide domain

+

+

+Taq polymerase <http://www.uniprot.org/uniprot/P19821>

+

+

+<http://www.ebi.ac.uk/interpro/entry/IPR019760>

+

+"""

+DNA polymerases (EC:2.7.7.7) can be classified, on the basis of sequence similarity [PMID: 3479792, PMID: 2196557], into at least four different groups: A, B, C and X. Members of family X are small (about 40 kDa) compared with other polymerases and encompass two distinct polymerase enzymes that have similar functionality: vertebrate polymerase beta (same as yeast pol 4), and terminal deoxynucleotidyl-transferase (TdT) (EC:2.7.7.31). The former functions in DNA repair, while the latter terminally adds single nucleotides to polydeoxynucleotide chains. Both enzymes catalyse addition of nucleotides in a distributive manner, i.e. they dissociate from the template-primer after addition of each nucleotide. DNA-polymerases show a degree of structural similarity with RNA-polymerases.

+

+Five regions of similarity are found in all the polymerases of this entry. The signature of this entry is to the conserved region, known as 'motif B' [PMID: 2196557]; motif B is located in a domain which, in E. coli polA, has been shown to bind deoxynucleotide triphosphate substrates; it contains a conserved tyrosine which has been shown, by photo-affinity labelling, to be in the active site; a conserved lysine, also part of this motif, can be chemically labelled, using pyridoxal phosphate.

+"""

+

+

+

+

+

+

+# Catalytic domain matching

+

+* RdRp catalytic domain matching <http://www.uniprot.org/saas/SAAS00519020> view all proteins annotated by this rule <http://www.uniprot.org/uniprot/?query=source:SAAS00519020>

+

+* * "Contains RdRp catalytic domain"

+

+* DdDp catalytic domain matching

+

+* RNA-directed RNA polymerase catalytic domain profiles <http://prosite.expasy.org/PDOC50507>

+

+* Reverse transcriptase (RT) catalytic domain profile <http://prosite.expasy.org/PDOC50878>

+

+

+

+

+

+* <https://en.wikipedia.org/wiki/Reverse_transcriptase>

+* <https://en.wikipedia.org/wiki/Telomerase_reverse_transcriptase>

+* <https://en.wikipedia.org/wiki/DNA_polymerase>

+* <https://en.wikipedia.org/wiki/RNA-dependent_RNA_polymerase>

+* <https://en.wikipedia.org/wiki/RNA_polymerase>

+* <https://en.wikipedia.org/wiki/Terminal_deoxynucleotidyl_transferase>

+

+

+"Flaviviruses produce a polyprotein from the ssRNA genome. The polyprotein is cleaved to a number of products, one of which is NS5. Recombinant dengue type 1 virus NS5 protein expressed in Escherichia coli exhibits RNA-dependent RNA polymerase activity. This RNA-directed RNA polymerase possesses a number of short regions and motifs homologous to other RNA-directed RNA polymerases.[11]"

+

+

+

+a template-independent polymerase like Terminal deoxynucleotidyl Transferase (TdT) or poly(A) polymerase

+

+"""

+According to certain aspects, oligonucleotide sequences may be prepared using ink jet techniques known to those of skill in the art, electrochemical techniques known to those of skill in the art, microfluidic techniques known to those of skill in the art, photogenerated acids known to those of skill in the art, or photodeprotected monomers known to those of skill in the art. Such techniques have the advantage of making oligonucleotides at high speed, low cost, fewer toxic chemicals, enhanced portability and ability to interleave DNA biochemistry (e.g. modifications, polymerases, hybridization etc.) with de novo (digital or analog) synthesis. For example, spatially patterned light, either directly from camera optics or from Digital Micromirror Display devices (DMD), can be used with aqueous chemistry. See US2003/0228611. For example, a template-independent polymerase like Terminal deoxynucleotidyl Transferase (TdT) or poly(A) polymerase—alternatively, a template-dependent polymerase like Taq or Phi29 derivatives, can have their basic polymerase function, base-specificity or fidelity programmable by light by incorporating an azobenzene amino acid (see Hoppmann C, Schmieder P, Heinrich N, Beyermann M. (2011) Chembiochem. 12(17):2555-9. doi: 10.1002/cbic. 201100578. Epub 2011 October 13, Photoswitchable click amino acids: light control of conformation and bioactivity) into the active site of the polymerase or 5′43′ exonuclease domains (if present).

+"""

+

+

+... can have their basic polymerase function, base-specificity or fidelity programmable by light by incorporating an azobenzene amino acid (see Hoppmann C, Schmieder P, Heinrich N, Beyermann M. (2011) Chembiochem. 12(17):2555-9. doi: 10.1002/cbic. 201100578. Epub 2011 October 13, Photoswitchable click amino acids: light control of conformation and bioactivity) into the active site of the polymerase or 5′43′ exonuclease domains

+

+

+see Hoppmann C, Schmieder P, Heinrich N, Beyermann M. (2011) Chembiochem. 12(17):2555-9. doi: 10.1002/cbic. 201100578. Epub 2011 October 13, Photoswitchable click amino acids: light control of conformation and bioactivity) into the active site of the polymerase or 5′43′ exonuclease domains

+

+"""

+Light sensitive neurons (optogenetics) can trigger ion-sensitive polymerases (see Zamft B, Marblestone A, Kording K, Schmidt D, Martin-Alarcon D, Tyo K, Boyden E, Church GM (2012) Measuring Cation Dependent DNA Polymerase Fidelity Landscapes by Deep Sequencing. PLoS One, in press) or, for some applications, the ion flux patterns themselves can constitute the stored datasets.

+"""

+

+

+"""

+The nucleotide type incorporated can be determined by: a) the intersection of a light pulse coincident with a particular dNTP (or rNTP or other monomer class) present at that time point in a cyclic pattern of dNTP solutions. b) ‘caged’ (i.e. photo-activatable or photo-inactivatable) dNTPs, rNTPs or cations. c) base-specific, light-modulated steric or conformational selectivity (see Hoppmann C, Schmieder P, Heinrich N, Beyermann M. (2011) Chembiochem. 12(17):2555-9. doi: 10.1002/cbic.201100578. Epub 2011 October 13. Photoswitchable click amino acids: light control of conformation and bioactivity). Poly(A) polymerase is particularly useful since its specificity for ATp relative to other rNTPs is due to a conformational change which can be mimicked by a photo-sensitive amino acid linkage (like azobenzene, with or without crosslinking).

+"""

+

+

+

+Photoswitchable Click Amino Acids: Light Control of Conformation and Bioactivity <http://onlinelibrary.wiley.com/doi/10.1002/cbic.201100578/abstract>

+

+"Click the switch: By using a photoswitchable click amino acid (PSCaa) a light-induced intramolecular thiol-ene click reaction with a neighboring cysteine under very mild conditions results in an azobenzene bridge (see figure). By expanding the genetic code for PSCaa the specific incorporation of photoswitch units into proteins in living cells can result in an exciting approach for studying light-controllable activity, in vivo."

+

+

+

+Reversible photocontrol of biological systems by the incorporation of molecular photoswitches

+

+Genetically encoding photoswitchable click amino acids in Escherichia coli and mammalian cells

+

+

+

+

+SELEX

+

+phage display

+

+ribosome display

+

+mRNA display

+

+phage-assisted continuous evolution

+

+TRAP display

+

+liposome display

+

+megavalent bead surface display

+

+mRNA display selection

+

+

+

+

+

+- azobenzene-matching aptamer, introduce azobenzene into the aqueous environment ?

+

+

+

+

+