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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 (a1)...

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.

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Corresponding author

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.

Keywords

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 (a1)...

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