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Predicting oligonucleotide affinity to nucleic acid targets

Published online by Cambridge University Press:  01 November 1999

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

Keywords

antisense oligonucleotidesbimolecular RNA secondary structurehybridizationprimer extensionreverse PCRreverse transcriptionRNA secondary-structure prediction
Type
Research Article
Information
RNA , Volume 5 , Issue 11 , November 1999 , pp. 1458 - 1469
Copyright
1999 RNA Society

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