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.
Publication types
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Research Support, Non-U.S. Gov't
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Research Support, U.S. Gov't, P.H.S.
MeSH terms
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Base Sequence
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Binding Sites
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Calorimetry
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DNA, Complementary / chemistry
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Globins / genetics
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Kinetics
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Models, Theoretical
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Molecular Sequence Data
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Nucleic Acid Conformation*
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Oligodeoxyribonucleotides / chemistry*
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Oligoribonucleotides / chemistry*
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RNA / chemistry*
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RNA, Complementary / chemistry
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RNA, Messenger / chemistry
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RNA, Messenger / genetics
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Ribonuclease H
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Software*
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Thermodynamics
Substances
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DNA, Complementary
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Oligodeoxyribonucleotides
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Oligoribonucleotides
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RNA, Complementary
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RNA, Messenger
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RNA
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Globins
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Ribonuclease H