title: Testing the nearest neighbor model for canonical RNA base pairs: revision of GU parameters.
abstract: Thermodynamic parameters for GU pairs are important for predicting the secondary structures of RNA and for finding genomic sequences that code for structured RNA. Optical melting curves were measured for 29 RNA duplexes with GU pairs to improve nearest neighbor parameters for predicting stabilities of helixes. The updated model eliminates a prior penalty assumed for terminal GU pairs. Six additional duplexes with the 5'GG/3'UU motif were added to the single representation in the previous database. This revises the ΔG°(37) for the 5'GG/3'UU motif from an unfavorable 0.5 kcal/mol to a favorable -0.2 kcal/mol. Similarly, the ΔG°(37) for the 5'UG/3'GU motif changes from 0.3 to -0.6 kcal/mol. The correlation coefficients between predicted and experimental ΔG°(37), ΔH°, and ΔS° for the expanded database are 0.95, 0.89, and 0.87, respectively. The results should improve predictions of RNA secondary structure.
authors.affiliation: Department of Chemistry, University of Rochester, Rochester, NY 14627, USA.
authors.forename: Jonathan L
authors.initials: JL
authors.lastname: Chen
authors.forename: Abigael L
authors.initials: AL
authors.lastname: Dishler
authors.forename: Scott D
authors.initials: SD
authors.lastname: Kennedy
authors.forename: Ilyas
authors.initials: I
authors.lastname: Yildirim
authors.forename: Biao
authors.initials: B
authors.lastname: Liu
authors.forename: Douglas H
authors.initials: DH
authors.lastname: Turner
authors.forename: Martin J
authors.initials: MJ
authors.lastname: Serra
mesh_terms: D020029:Base Pairing; D001483:Base Sequence; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry*; D013816:Thermodynamics
chemical_list: D012313:RNA