Predicting oligonucleotide affinity to nucleic acid targets.
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.
Mathews
D H
DH
Department of Chemistry, University of Rochester, New York 14627-0216, USA.
Burkard
M E
ME
Freier
S M
SM
Wyatt
J R
JR
Turner
D H
DH
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
D018076:DNA, Complementary; D009838:Oligodeoxyribonucleotides; D009843:Oligoribonucleotides; D018075:RNA, Complementary; D012333:RNA, Messenger; D012313:RNA; D005914:Globins; D016914:Ribonuclease H