Hostname: page-component-7c8c6479df-nwzlb Total loading time: 0 Render date: 2024-03-28T17:48:18.300Z Has data issue: false hasContentIssue false

Predicting oligonucleotide affinity to nucleic acid targets

Published online by Cambridge University Press:  01 November 1999

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
Get access

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.

Type
Research Article
Copyright
1999 RNA Society

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)