A computer program for choosing optimal oligonucleotides for filter hybridization, sequencing and in vitro amplification of DNA.

W Rychlik; R E Rhoads

doi:10.1093/nar/17.21.8543

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A computer program for choosing optimal oligonucleotides for filter hybridization, sequencing and in vitro amplification of DNA.

W Rychlik·R E Rhoads

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Abstract

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.

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Base Sequence DNA Electrophoresis, Agar Gel Gene Amplification Molecular Sequence Data Nucleic Acid Hybridization Oligonucleotide Probes Oligonucleotides Software Journal Article Research Support, U.S. Gov't, P.H.S.

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W Rychlik, R E Rhoads. 1989-11-11. A computer program for choosing optimal oligonucleotides for filter hybridization, sequencing and in vitro amplification of DNA.. https://doi.org/10.1093/nar%2F17.21.8543

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