title: Coaxial stacking of helixes enhances binding of oligoribonucleotides and improves predictions of RNA folding.
abstract: An RNA model system consisting of an oligomer binding to a 4-nt overhang at the 5' end of a hairpin stem provides thermodynamic parameters for helix-helix interfaces. In a sequence-dependent manner, oligomers bind up to 1000-fold more tightly adjacent to the hairpin stem than predicted for binding to a free tetramer at 37 degrees C. For the interface (/) in [formula: see text] additional free energy change, delta delta G 37 degrees, for binding is roughly the nearest-neighbor delta G 37 degrees for propagation of an uninterrupted helix of equivalent sequence, CGGC. When X and Z are omitted, the delta delta 37 degrees is even more favorable by approximately 1 kcal/mol (1 cal = 4.184J). On average, predictions of 11 RNA secondary structures improve from 67 to 74% accuracy by inclusion of similar stacking contributions.
authors.affiliation: Department of Chemistry, University of Rochester, NY 14627-0216.
authors.forename: A E
authors.initials: AE
authors.lastname: Walter
authors.forename: D H
authors.initials: DH
authors.lastname: Turner
authors.forename: J
authors.initials: J
authors.lastname: Kim
authors.forename: M H
authors.initials: MH
authors.lastname: Lyttle
authors.forename: P
authors.initials: P
authors.lastname: Müller
authors.forename: D H
authors.initials: DH
authors.lastname: Mathews
authors.forename: M
authors.initials: M
authors.lastname: Zuker
mesh_terms: D000818:Animals; D001483:Base Sequence; D002151:Calorimetry; D007438:Introns; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009843:Oligoribonucleotides / Q000737:chemistry*; D010802:Phylogeny; D012313:RNA / Q000737:chemistry* / Q000235:genetics; D012329:RNA, Bacterial / Q000737:chemistry; D012331:RNA, Fungal / Q000737:chemistry; D051381:Rats; D013329:Structure-Activity Relationship
chemical_list: D009843:Oligoribonucleotides; D012329:RNA, Bacterial; D012331:RNA, Fungal; D012313:RNA