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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)
  • Published online: 01 November 1999
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.

Copyright
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.
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RNA
  • ISSN: 1355-8382
  • EISSN: 1469-9001
  • URL: /core/journals/rna
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