A computer program for choosing optimal oligonucleotides for filter hybridization, sequencing and in vitro amplification of DNA.
A method is presented for choosing optimal oligodeoxyribonucleotides as probes for filter hybridization, primers for sequencing, or primers for DNA amplification. Three main factors that determine the quality of a probe are considered: stability of the duplex formed between the probe and target nucleic acid, specificity of the probe for the intended target sequence, and self-complementarity. DNA duplex stability calculations are based on the nearest-neighbor thermodynamic values determined by Breslauer et al. [Proc. Natl. Acad. Sci. U.S.A. (1986), 83: 3746]. Temperatures of duplex dissociation predicted by the method described here were within 0.4 degrees C of the values obtained experimentally for ten oligonucleotides. Calculations for specificity of the probe and its self-complementarity are based on a simple dynamic algorithm.
Rychlik
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Department of Biochemistry, University of Kentucky, Lexington 40536.
Rhoads
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D001483:Base Sequence; D004247:DNA / Q000235:genetics*; D004587:Electrophoresis, Agar Gel; D005784:Gene Amplification; D008969:Molecular Sequence Data; D009693:Nucleic Acid Hybridization; D015345:Oligonucleotide Probes; D009841:Oligonucleotides; D012984:Software
D015345:Oligonucleotide Probes; D009841:Oligonucleotides; D004247:DNA