Abstract
While it is possible to perform molecular systematic studies without the Poly-merase Chain reaction (PCR; [1]), there is no doubt that PCR is responsible for the tremendous explosion of the field, both in terms of the number of sequences generated and the number of taxa which have been sampled. This technique, which at its most basic can be accomplished with three water baths, a pair of hands and the necessary reagents, has made it possible to quickly and easily search entire genomes for particular sequences. Researchers using PCR have extracted genetic information from ancient samples (reviewed in [2]; see also “Enjoy 577 Ancient DNA references (or even more)” http://www.comic.sbg.ac.at/staff/jan/ancient/references.htm) and as minimal a starting material as a single cell [3]. Its effect has been felt in all fields of biology ranging from medicine and forensic science to ecology and evolutionary biology.
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References
Mullis K, Faloona F, Scharf S, Saiki Retal. (1986) Specific enzymatic amplification of DNA in vitro: the polymerase chain reaction. Cold Spring Harbor Symposia on Quantitative Biology 51: 263–273
DeSalle R, Bonwich E (1996) DNA isolation, manipulation and characterization form old tissues.Genetic Engineering 18: 13–32
Zhang L, Cui X, Schmitt K, Hubert R et al. (1992) Whole genome amplification from a single cell: implications for genetic analysis. Proc. Natl. Acad. Sci. USA 89: 5847–5851
Saiki RK, Gelfand DH, Stoeffel S, Scharf S et al. (1988) Primer directed amplification of DNA with a thermostable DNA polymerase. Science 239: 487–491
Innis MA, Gelfand DH, Sninsky JJ (eds.) (1990) PCR Prtocols:A Guide to Meth-ods and Applications. Academic Press, San Diego
Sonnenfeld M, Ward, Nystrom, Mosher G, Stahl J et al. (1997) The Drosophila tango gene encodes a bHLH-PAS protein that is orthologous to mammalian Arnt and contols CNS midline and tracheal development. Development 124: 4571–4582
Helmsley A, Arnheim N, Toney MD, Cortopassi G et al. (1989) A simple method for site-directed mutagenesis using the polymerase chain reaction. Nucleic Acid Res. 17: 6545–51
Nasidze I, M. Stoneking. 1999. Short Technical Reports: Construction of larger-size sequencing templates from degraded DNA. Biotechniques 27 (September): 480–88
Amato G, Gatesy J (1994) PCR assays of variable nucleotide sites for identification of conservation units. In: B Schierwater, B Streit, GP Wagner and R DeSalle (eds) Molecular Ecology and Evolution: Approaches and Applications Birkhauser Verlag, Basel/Switzerland
Selvakumar N, Ding B, Wilson SM (1997) Improved resolution of asymmetric-PCR SSCP Products. Biotechniques 22: 606–608
Sellner LN, Turbett GR (1998) Comparison of three RT-PCR methods. Biotechniques 25 (August): 230–234
Chadwick N, Wakefield J, Pounder RE, Bruce IJ (1998) Comparison of Three RNA Amplification Methods as Sources of DNA for Sequencing. Biotechniques 25 (November): 818–822
Barnes WM (1994) PCR amplification of up to 35-kb DNA with high fidelity and high yield from lambda bacteriophage templates. Proc. Natl. Acad. Sci. USA 91: 2216–2220
Cheng S, Fockler C, Barnes WM and Higuchi R (1997) Effective amplification of long targets from cloned inserts and human genomic DNA. Proc. Natl. Acad. Sci. USA 91: 5695–5699
Min G, Powell JR (1998) Long-Distance Genome Walking Using the Long and Accurate Polymerase Chain Reaction. Biotechniques 24 (March): 398–400
Sanchez-Cespedes M, Cairns P, Jen J, Sidransky D (1998) Degenerate Oligonucleotide-Primed PCR (DOP-PCR): evaluation of its reliability for screening of genetic alterations in neoplasia. Biotechniques 25 (December): 1036–1038
Suazo A, Hall HG (1999) Modification of the AFLP Protocol Applied to Honey Bee (Apis mellifera L.) DNA. Biotechniques 26 (April): 704–709
Vos P, Hogers R, Bleeker M, Reijans M et al. (1995) AFLP: A new technique for DNA fingerprinting. Nucleic Acids Res. 21: 4407–4414
Reineke A, Karlovsky P (2000) Simplified AFLP Protocol: Replacement of primer labeling by the incorporation of a-labeled nucleotides during PCR. Biotechniques 28 (April): 622–623
Schupp JM, Price LB, Klevytska A, Keim P (1999) Internal and flanking sequence from AFLP Fragments Using Ligation - Mediated Suppression PCR. Biotechniques 26 (May): 905–912
Lin J-J, Ma J, Kuo J (1999) Chemiluminescent detection of AFLP markers. Biotechniques 26 (February): 344–348
Atienzar F, Evenden A, Jha A, Sawa D et al. (2000) Optimized RAPD analysis generates high - quality genomic DNA profiles at high annealing temperature. Biotechniques 28 (January): 52–54
Ellinghaus P, Badehorn D, Blümer R, Becker K et al. (1999) Increased efficiency of arbitrarily primed PCR by prolonged ramp times. Biotechniques 26 (April): 626–630
Corley-Smith GE, Lim CJ, Kalmar GB, Brandhorst B (1997) Efficient Detection of DNA Polymorphisms by Fluorescent RAPD Analysis. Biotechniques 22 (April): 690–699
Pan Y-B, Burner DM, Ehrlich KC, Grisham MP et al. (1997) Analysis of primer - derived, nonspecific Amplification products in RAPD - PCR. Biotechniques 22 (June): 1071–1077
Gallego FJ and Martinez I (1997) Method to improve reliability of random - amplified polymorphic DNA markers. Biotechniques 23 (October): 663–664
Ramser J, Weising K, Chikaleke V, Kahl G (1997) Increased informativeness of RAPD analysis by detection of microsatellite Motifs. Biotechniques 23 (August): 285–290
Leamon JH, Moiseff A, Crivello JF (2000) Development of a high - throughput process for detection and screening of genetic polymorphisms. Biotechniques 28 (May): 994–1005
Williams JGK, Kubelik AR, Livak KJ, Rafalski JA (1990) DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Res. 25: 6531–6535
Rieseberg LH (1996) Homology among RAPD fragments in interspecific comparisons. Mol. Ecol. 5: 99–105
Varadaraj K, Skinner DM (1994) Denaturants or cosolvents improve the specificity of PCR amplification of a G+C rich DNA using genetically engineered DNA polymerases. Gene 140: 1–5
Rees WA, Yager TD, Korte J, von Hippel PH (1993) Betaine can eliminate the base pair composition dependence of DNA melting. Biochemistry 32: 137–144
Melchior WB and von Hippel PH (1973) Alteration of the relative stability ofdA•dT and dG•dC base pairs in DNA. Proc. Nat. Acad. Sci. USA. 70: 298–302
Henke W, Herdel K, Jung K, Schnorr D et al. (1997) Betaine improves the PCR amplification of GC-rich DNA sequences. Nucleic Acids Research. 25: 3957–3958
Baskaran N, Kandpal RP, Bhargava AK, Glynn MW et al. (1996) Uniform amplification of a mixture of deoxyribonucleic acids with varying GC content. Genome Research 6: 633–638
Chevet E, Lemaitre G, Katinka D (1995) Low concentrations of tetramethylammoniumchloride increase yield and specificity of PCR. Nucleic Acids Research 23: 3343–3344
McConlogue L, Brow MA, Innis MA (1988) Structure independent DNA amplification of PCR using 7-deaza-2’-deoxyguanosine. Nucleic Acids Research 16: 9869
Sarkar G, Kapelner S, Sommer SS (1990) Formamide can dramatically improve the specificity of PCR. Nucleic Acids Research 18: 7465
Stommel JR, Panta GR, Levi A, Rowland LJ (1997) Effects of gelatin and BSA on the amplification reaction for generating RAPD. Biotechniques 22: 1064–1066
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Bonacum, J., Stark, J., Bonwich, E. (2002). PCR Methods and Approaches. In: DeSalle, R., Giribet, G., Wheeler, W. (eds) Techniques in Molecular Systematics and Evolution. Methods and Tools in Biosciences and Medicine. Birkhäuser, Basel. https://doi.org/10.1007/978-3-0348-8125-8_14
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DOI: https://doi.org/10.1007/978-3-0348-8125-8_14
Publisher Name: Birkhäuser, Basel
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