Abstract
The Polymerase Chain Reaction process is a well-known technique for the in vitro amplification of a DNA sequence. The success of a PCR depends on several parameters particularly the primer sequences used. Since the design of a suitable pair of primer involves a reasonable number of variables, which can have a range of different values, computer programs are commonly used to assist this task. This paper approaches the design of a pair of primer sequences as a search process throughout the space defined by all possible primer sequence pairs, directed by an evaluation function that combines the many variables involved in a primer design; an experiment and its results are discussed.
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Mullis, K.B., Faloona, F.: Specific synthesis of DNA in vitro via a polymerase-catalyzed chain reaction. Methods Enzymology 155, 335–350 (1987)
Metzker, M.L., Caskey, T.C.: Polymerase Chain Reaction (PCR), Encyclopedia of Life Science. Nature Publishing Group (2001)
Innis, M.A., Gelfand, D.H.: Optimization of PCRs. In: Innis, Gelfand, Sninsky, White (eds.) PCR Protocols. Academic Press, New York (1990)
Kamel, A., Abd-Elsalam: Bioinformatic tools and guideline for PCR primer design. African Journal of Biotechnology 2(5), 91–95 (2003)
Kwok, S., Kellogg, D.E., McKinney, N., Spasic, D., Goda, L., Levenson, C., Sninsky, J.: Effects of primer-template mismatches on the polymerase chain reaction: Human Immunodeficiency Virus 1 model studies. Nucleic Acids Research 18, 999–1005 (1990)
Wallace, R.B., Shaffer, J., Murphy, R.F., Bonner, J., Hirose, T., Itakura, K.: Hybridization of synthetic oligodeoxyribonucleotides to phi chi 174 DNA: the effect of single base pair mismatch. Nuclic Acids Research 6, 3543–3557 (1979)
Marmur, J., Doty, P.: Determination of the base composition of deoxyribonucleic acid from its thermal denaturation temperature. Journal of Molecular Biology 5, 109–118 (1962)
Howley, P.M., Israel, M.F., Law, M.-F., Martin, M.A.: A rapid method for detecting and mapping homology between heterologous DNAs. Journal of Biological Chemistry 254, 4876–4883 (1979)
Breslauer, K.J., Frank, R., Blocker, H., Marky, L.A.: Predicting DNA duplex stability from the base sequence. Proc. Natl. Acad. Sci. USA 83, 3746–3750 (1986)
Sugimoto, N., Nakano, S., Yoneyama, M., Honda, K.: Improved thermodynamic parameters and helix initiation factor to predict stability of DNA duplexes. Nucleic Acids Research 24, 4501–4505 (1996)
SantaLucia Jr., J., Allawi, H.T., Seneviratne, P.A.: Improved Nearest-Neighbor parameters for predicting DNA duplex stability. Biochemistry 35, 3555–3562 (1996)
Rychlik, W., Spencer, W.J., Rhoads, R.E.: Optimization of the annealing temperature for DNA amplification in vitro. Nucleic Acids Research 18, 6409–6412 (1990)
Kämpke, T., Kieninger, M., Mecklenbug, M.: Efficient primer design algorithms. Bioinformatics 17(3), 214–225 (2001)
Panjkovich, A., Melo, F.: Comparison of different melting temperature calculation methods for short DNA sequences. Bioinformatics 21(6), 711–722 (2005)
Kirkpatrick, S., Gelatt, C.D., Vecchi, M.P.: Optimization by simulated annealing. Science 220, 671–680 (1983)
He, Q., Marjamäki, M., Soini, H., Mertsola, J., Viljanen, M.K.: Primers are decisive for sensitivity of PCR. BioTechniques 17(1), 82–87 (1994)
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Montera, L., Nicoletti, M.C. (2008). The PCR Primer Design as a Metaheuristic Search Process. In: Rutkowski, L., Tadeusiewicz, R., Zadeh, L.A., Zurada, J.M. (eds) Artificial Intelligence and Soft Computing – ICAISC 2008. ICAISC 2008. Lecture Notes in Computer Science(), vol 5097. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-69731-2_91
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DOI: https://doi.org/10.1007/978-3-540-69731-2_91
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