RNA



Predicting oligonucleotide affinity to nucleic acid targets


DAVID H.  MATHEWS a1, MARK E.  BURKARD a1, SUSAN M.  FREIER a2, JACQUELINE R.  WYATT a2 and DOUGLAS H.  TURNER a1c1
a1 Department of Chemistry, University of Rochester, Rochester, New York 14627-0216, USA
a2 Division of Molecular and Structural Biology, Isis Pharmaceuticals, Carlsbad, California 92008, USA

Abstract

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.

Correspondence:
c1 Reprint requests to: Douglas H. Turner, Department of Chemistry, University of Rochester, Rochester, New York 14627-0216, USA; e-mail: turner@chem.chem.rochester.edu.