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rna secondary-structure prediction

RNA (1)

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Predicting oligonucleotide affinity to nucleic acid targets
DAVID H. MATHEWS, MARK E. BURKARD, SUSAN M. FREIER, JACQUELINE R. WYATT, DOUGLAS H. TURNER
Journal:

RNA / Volume 5 / Issue 11 / November 1999

Published online by Cambridge University Press:

01 November 1999, pp. 1458-1469

Print publication:

November 1999
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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.