Abstract
Although many factors influence the results of a DNA sequencing or PCR reaction, the most important are the quality of the template and the choice of the oligonucleotides. In this chapter I give an overview of how to design oligonucleotides that could be used as primers for DNA sequencing and/or for PCR reactions by using the computer program PRIME. For efficient priming, one should avoid primers with extensive self-complementarity in order to minimize primer secondary structures and dimer formations. Computer programs calculate hybridization temperatures and secondary structures based on the highly accurate measurement of nearest-neighbor ΔG (change in free energy) values.
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References
Devereux, J., Haeberli, P., and Smithies, O. (1984) A comprehensive set of sequence analysis programs for the VAX. Nucleic Acids Res. 12, 387–395.
Dölz, R. (1994) GCG, in Computer Analysis Of Sequence Data, Methods In Molecular Biology, vol. 25 (Griffin, A. M. and Griffin, H. G., eds.), Humana, Totowa, NJ, pp. 9–17.
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© 1997 Humana Press Inc.
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Estruch, J.J. (1997). PRIME. In: Swindell, S.R. (eds) Sequence Data Analysis Guidebook. Methods In Molecular Medicine™, vol 70. Springer, Totowa, NJ. https://doi.org/10.1385/0-89603-358-9:287
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DOI: https://doi.org/10.1385/0-89603-358-9:287
Publisher Name: Springer, Totowa, NJ
Print ISBN: 978-0-89603-358-0
Online ISBN: 978-1-59259-556-3
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