SpringerProtocols: Abstract: 2. Computer Programs for PCR Primer Design and Analysis

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2. Computer Programs for PCR Primer Design and Analysis

By: Bing-Yuan Chen², Harry W. Janes², Steve Chen³

Abstract

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Heat will separate or &quote;melt&quote; double-stranded DNA into single-stranded DNA by disrupting its hydrogen bonds. T _m (melting temperature) is the temperature at which half the DNA strands are single-stranded and half are double-stranded. T _m characterizes the stability of the DNA hybrid formed between an oligonucleotide and its complementary strand and therefore is a core parameter in primer design. It is affected by primer length, primer sequence, salt concentration, primer concentration, and the presence of denaturants (such as formamide or DMSO).

Affiliation(s): (2) Department of Plant Science, Rutgers University, New Brunswick, NJ
(3) NetOsprey Inc., Berkeley, CA

Book Title: PCR Cloning Protocols

Series: Methods in Molecular Biology | Volume: 192 | Pub. Date: Apr-01-2002 | Page Range: 19-29 | DOI: 10.1385/1-59259-177-9:019

Subject: Genetics/Genomics

References

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2.	Rychlik, W. and Rhoads, R. E. (1989) A computer program for choosing optimal oligo-nucleotides for filter hybridization, sequencing and in vitro amplification of DNA. Nucl. Acids Res. 17, 8543–8551.

3.	Wu, D. Y., Ugozzoli, L., Pal, B. K., Qian, J., and Wallace, R. B. (1991) The effect of temperature and oligonucleotide primer length on the specificity and efficiency of amplification by the polymerase chain reaction. DNA Cell Biol. 10, 233–238.

4.	Rychlik, W. (1993) Selection of primers for polymerase chain reaction, in PCR Protocols. Current Methods and Applications (White, B. A., ed.), Humana, Totowa, NJ, pp. 31–40.

5.	Innis, M. A. and Gelfand, D. H. (1990) Optimization of PCRs, in PCR Protocols (Innis, M. A., Gelfand, D. H., Sninsky, J. J., and White, T. J., eds.), Academic, New York, pp. 3–12.

6.	Breslauer, K. J., Frank, R., Blocker, H., and Markey, L. A. (1986) Predicting DNA duplex stability from the base sequence. Proc. Natl. Acad. Sci. USA 83, 3746–3750.

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