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.

Copper(II)–Thymine Coordination Polymer Nanoribbons as Potential Oligonucleotide Nanocarriers

“…We have also observed that the interaction between 1n and PolyC or PolyG is higher than that with PolyT. [12] These results support the potential use of CPs bearing modified nucleobases as platforms for the interaction with oligonucleotides by conventional Watson-Crick base pairs and/or more complex interactions such as non-canonical base pairs and metal-nucleobase interactions.T otest the biocompatibility of 1nwe evaluated its toxicity in different cell lines using the resazurin assay. [12] These results support the potential use of CPs bearing modified nucleobases as platforms for the interaction with oligonucleotides by conventional Watson-Crick base pairs and/or more complex interactions such as non-canonical base pairs and metal-nucleobase interactions.T otest the biocompatibility of 1nwe evaluated its toxicity in different cell lines using the resazurin assay.…”

Structure of RNA Stem Loop B from the Picornavirus Replication Platform

“…41 The average observed shear value for the G4-U21 wobble base pair (approximately −1.9 Å) is a feature consistent with wobble base pairs presented in the literature, as are unusual twist parameters near a G-U pair. 42–47 The observed twists can be characterized as an overtwisting of the helix at the G4/A5 step and an undertwisting at the next step, A5/U6. Ananth et al report that overtwisting (~47°) is common at Watson–Crick (WC)/GU base pair steps while undertwisting is often observed in the next base pair step (GU/WC ~ 19°).…”

“…Ananth et al report that overtwisting (~47°) is common at Watson–Crick (WC)/GU base pair steps while undertwisting is often observed in the next base pair step (GU/WC ~ 19°). 42 However, the overtwisting and undertwisting near a G-U pair is often reported at different positions. For instance, Joli et al reported the WC/GU base pair step experiences an under-twisting while the GU/WC step is slightly overtwisted.…”

The multiple flavors of GoU pairs in RNA

“…During the evolutionary processes, GoU pairs are therefore ideal transient pairs appearing between Watson‐Crick pairs in aligned sequences . Thus, in sequence alignments, conserved GoU pairs indicate a specific role either structural (stabilization) or functional as discussed above (see also Ananth et al and Mokdad et al).…”