title: 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.
authors.affiliation: Department of Chemistry, University of Rochester, New York 14627-0216, USA.
authors.forename: D H
authors.initials: DH
authors.lastname: Mathews
authors.forename: M E
authors.initials: ME
authors.lastname: Burkard
authors.forename: S M
authors.initials: SM
authors.lastname: Freier
authors.forename: J R
authors.initials: JR
authors.lastname: Wyatt
authors.forename: D H
authors.initials: DH
authors.lastname: Turner
mesh_terms: D001483:Base Sequence; D001665:Binding Sites; D002151:Calorimetry; D018076:DNA, Complementary / Q000737:chemistry; D005914:Globins / Q000235:genetics; D007700:Kinetics; D008962:Models, Theoretical; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009838:Oligodeoxyribonucleotides / Q000737:chemistry*; D009843:Oligoribonucleotides / Q000737:chemistry*; D012313:RNA / Q000737:chemistry*; D018075:RNA, Complementary / Q000737:chemistry; D012333:RNA, Messenger / Q000737:chemistry / Q000235:genetics; D016914:Ribonuclease H; D012984:Software; D013816:Thermodynamics
chemical_list: D018076:DNA, Complementary; D009838:Oligodeoxyribonucleotides; D009843:Oligoribonucleotides; D018075:RNA, Complementary; D012333:RNA, Messenger; D012313:RNA; D005914:Globins; D016914:Ribonuclease H