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An innate twist between Crick’s wobble and Watson-Crick base pairs

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 sim...

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Detalles Bibliográficos
Autores principales: Ananth, Prakash, Goldsmith, Gunaseelan, Yathindra, Narayanarao
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Cold Spring Harbor Laboratory Press 2013
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3708525/
https://www.ncbi.nlm.nih.gov/pubmed/23861536
http://dx.doi.org/10.1261/rna.036905.112
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author Ananth, Prakash
Goldsmith, Gunaseelan
Yathindra, Narayanarao
author_facet Ananth, Prakash
Goldsmith, Gunaseelan
Yathindra, Narayanarao
author_sort Ananth, Prakash
collection PubMed
description 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.
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spelling pubmed-37085252014-08-01 An innate twist between Crick’s wobble and Watson-Crick base pairs Ananth, Prakash Goldsmith, Gunaseelan Yathindra, Narayanarao RNA Reviews 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. Cold Spring Harbor Laboratory Press 2013-08 /pmc/articles/PMC3708525/ /pubmed/23861536 http://dx.doi.org/10.1261/rna.036905.112 Text en © 2013; Published by Cold Spring Harbor Laboratory Press for the RNA Society http://creativecommons.org/licenses/by-nc/3.0/ This article is distributed exclusively by the RNA Society for the first 12 months after the full-issue publication date (see http://rnajournal.cshlp.org/site/misc/terms.xhtml). After 12 months, it is available under a Creative Commons License (Attribution-NonCommercial 3.0 Unported), as described at http://creativecommons.org/licenses/by-nc/3.0/.
spellingShingle Reviews
Ananth, Prakash
Goldsmith, Gunaseelan
Yathindra, Narayanarao
An innate twist between Crick’s wobble and Watson-Crick base pairs
title An innate twist between Crick’s wobble and Watson-Crick base pairs
title_full An innate twist between Crick’s wobble and Watson-Crick base pairs
title_fullStr An innate twist between Crick’s wobble and Watson-Crick base pairs
title_full_unstemmed An innate twist between Crick’s wobble and Watson-Crick base pairs
title_short An innate twist between Crick’s wobble and Watson-Crick base pairs
title_sort innate twist between crick’s wobble and watson-crick base pairs
topic Reviews
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3708525/
https://www.ncbi.nlm.nih.gov/pubmed/23861536
http://dx.doi.org/10.1261/rna.036905.112
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