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Computer Programs for PCR Primer Design and Analysis

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PCR Cloning Protocols

Part of the book series: Methods in Molecular Biology™ ((MIMB,volume 192))

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Abstract

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).

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References

  1. Wallace, R. B., Shaffer, J., Murphy, R. F., Bonner, J., Hirose, T., and Itakura, K. (1979) Hybridization of synthetic oligodeoxyribonucleotides to phi chi 174 DNA: the effect of single base pair mismatch. Nucl. Acids Res. 6, 3543–3557.

    Article  CAS  PubMed  Google Scholar 

  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.

    Article  CAS  PubMed  Google Scholar 

  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.

    Article  CAS  PubMed  Google Scholar 

  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.

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  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.

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  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.

    Article  CAS  PubMed  Google Scholar 

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© 2002 Humana Press Inc.

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Chen, BY., Janes, H.W., Chen, S. (2002). Computer Programs for PCR Primer Design and Analysis. In: Chen, BY., Janes, H.W. (eds) PCR Cloning Protocols. Methods in Molecular Biology™, vol 192. Humana Press. https://doi.org/10.1385/1-59259-177-9:019

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  • DOI: https://doi.org/10.1385/1-59259-177-9:019

  • Publisher Name: Humana Press

  • Print ISBN: 978-0-89603-969-8

  • Online ISBN: 978-1-59259-177-0

  • eBook Packages: Springer Protocols

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