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Predicting oligonucleotide affinity to nucleic acid targets.

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.

SUBMITTER: Mathews DH

PROVIDER: S-EPMC1369867 | biostudies-other | 1999 Nov

REPOSITORIES: biostudies-other

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Predicting oligonucleotide affinity to nucleic acid targets.

Mathews D H DH Burkard M E ME Freier S M SM Wyatt J R JR Turner D H DH

RNA (New York, N.Y.) 19991101 11

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 com ...[more]

PMID: 10580474

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