title: An innate twist between Crick's wobble and Watson-Crick base pairs.
abstract: Non-Watson-Crick pairs like the G·U wobble are frequent in RNA duplexes. Their geometric dissimilarity (nonisostericity) with the Watson-Crick base pairs and among themselves imparts structural variations decisive for biological functions. Through a novel circular representation of base pairs, a simple and general metric scheme for quantification of base-pair nonisostericity, in terms of residual twist and radial difference that can also envisage its mechanistic effect, is proposed. The scheme is exemplified by G·U and U·G wobble pairs, and their predicable local effects on helical twist angle are validated by MD simulations. New insights into a possible rationale for contextual occurrence of G·U and other non-WC pairs, as well as the influence of a G·U pair on other non-Watson-Crick pair neighborhood and RNA-protein interactions are obtained from analysis of crystal structure data. A few instances of RNA-protein interactions along the major groove are documented in addition to the well-recognized interaction of the G·U pair along the minor groove. The nonisostericity-mediated influence of wobble pairs for facilitating helical packing through long-range interactions in ribosomal RNAs is also reviewed.
authors.affiliation: Institute of Bioinformatics and Applied Biotechnology, Bangalore 560100, Karnataka, India.
authors.forename: Prakash
authors.initials: P
authors.lastname: Ananth
authors.forename: Gunaseelan
authors.initials: G
authors.lastname: Goldsmith
authors.forename: Narayanarao
authors.initials: N
authors.lastname: Yathindra
mesh_terms: D020029:Base Pairing; D001665:Binding Sites; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry*; D016601:RNA-Binding Proteins / Q000737:chemistry
chemical_list: D016601:RNA-Binding Proteins; D012313:RNA
keywords: non-Watson-Crick pairs; nonisosteric base pairs; radial difference; residual twist; self-isosteric base pairs; wobble pairs