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. 1999 Nov;5(11):1458-69.
doi: 10.1017/s1355838299991148.

Predicting oligonucleotide affinity to nucleic acid targets

D H Mathews  1 , M E Burkard, S M Freier, J R Wyatt, D H Turner
Affiliations

Predicting oligonucleotide affinity to nucleic acid targets

D H Mathews et al. RNA. 1999 Nov.

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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