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

Nucleic Acids Res. 1989 Nov 11;17(21):8543-51. doi: 10.1093/nar/17.21.8543.


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.

Publication types

  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Base Sequence
  • DNA / genetics*
  • Electrophoresis, Agar Gel
  • Gene Amplification*
  • Molecular Sequence Data
  • Nucleic Acid Hybridization
  • Oligonucleotide Probes
  • Oligonucleotides*
  • Software*


  • Oligonucleotide Probes
  • Oligonucleotides
  • DNA