Page designed and maintained by Octavian Henegariu (Email: or ). As I am currently pursuing a new junior faculty position, the Yale URL and email may change in the near future. If messages sent to the "yale.edu" address bounce back to you, please send them again to the "yahoo.com" address. WARNING: The information provided in these pages is copyrighted and is intended for individual use only. No parts of this work (text, tables or pictures) may be commercialized, published or otherwise reproduced without the written consent of the author. For a complete description of primers, PCR programs and a discussion of the PCR conditions please consult: Andrologia 26: 97-106 (1994) and Biotechniques 23: 504-511 (1997). Click here to get the Biotechniques paper in PDF format. PCR page | PCR guide | PCR troubleshooting | Standards | Applications | Tavi's Home New links !! --> FISH page | CCK procedure | Nucleotide labeling | Slide preparation PCR and multiplex PCR guide Table below lists the parameters influencing the PCR reaction and indicates some PCR and multiplex PCR applications. Clicking on an item in the table, will take you to a detailed page, describing that particular issue. Topics for PCR optimization 0. Standards: examples of multiplex reactions used in all experiments 1 Generalities Components, PCR cycle, vials 9 Annealing time and temperature 2 Choosing PCR primers How to design the primers 10 Extension time and temperature 3 Reaction volumes Do they influence the results? 11 DNA template concentration 4 Number of PCR products Multiplexing. How ? 12 Taq polymerase(s) Comparisons and concentration 5 Primer amount How much primer? 13 dNTP concentration Interaction with magnesium 6 PCR buffers Comparisons and concentration 14 MgCl2 concentration Interaction with dNTP and salt (PCR buffer) 7 Salt (KCl) concentration Essential optimization factor 15 Gel electrophoresis Agarose and polyacrylamide (PAA) 8 Designing PCR programs Customize them for your purpose 16 Adjuvants in PCR DMSO, glycerol and BSA Some applications of PCR and multiplex PCR A Microdeletion screening D PCR labeling B LOH E InterAlu-PCR C Quantitative multiplex PCR* F Degenerative priming PCR