Predicting oligonucleotide affinity to nucleic acid targets

A computer program, OligoWalk, is reported that predicts the equilibrium af finity of complementary DNA or RNA oligonucleotides to an RNA target. This program considers the predicted stability of the oligonucleotide-target hel ix and the competition with predicted secondary structure of both the targe t and the oligonucleotide, Both unimolecular and bimolecular oligonucleotid e self structure are considered with a user-defined concentration. The appl ication of OligoWalk is illustrated with three comparisons to experimental results drawn from the literature.