Predicting oligonucleotide affinity to nucleic acid targets
A computer program, OligoWalk, is reported that predicts the equilibrium affinity of complementary DNA or RNA oligonucleotides to an RNA target. This program considers the predicted stability of the oligonucleotide-target helix and the competition with predicted secondary structure of both the target and the oligonucleotide. Both unimolecular and bimolecular oligonucleotide self structure are considered with a user-defined concentration. The application of OligoWalk is illustrated with three comparisons to experimental results drawn from the literature.(Received June 2 1999)
(Revised July 2 1999)
(Accepted August 16 1999)
Key Words: antisense oligonucleotides; bimolecular RNA secondary structure; hybridization; primer extension; reverse PCR; reverse transcription; RNA secondary-structure prediction.
c1 Reprint requests to: Douglas H. Turner, Department of Chemistry, University of Rochester, Rochester, New York 14627-0216, USA; e-mail: firstname.lastname@example.org.