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The Annotation of RNA Motifs

The recent deluge of new RNA structures, including complete atomic-resolution views of both subunits of the ribosome, has on the one hand literally overwhelmed our individual abilities to comprehend the diversity of RNA structure, and on the other hand presented us with new opportunities for compreh...

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Detalles Bibliográficos
Autores principales: Leontis, Neocles B., Westhof, Eric
Formato: Texto
Lenguaje:English
Publicado: Hindawi Publishing Corporation 2002
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2448414/
https://www.ncbi.nlm.nih.gov/pubmed/18629252
http://dx.doi.org/10.1002/cfg.213
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author Leontis, Neocles B.
Westhof, Eric
author_facet Leontis, Neocles B.
Westhof, Eric
author_sort Leontis, Neocles B.
collection PubMed
description The recent deluge of new RNA structures, including complete atomic-resolution views of both subunits of the ribosome, has on the one hand literally overwhelmed our individual abilities to comprehend the diversity of RNA structure, and on the other hand presented us with new opportunities for comprehensive use of RNA sequences for comparative genetic, evolutionary and phylogenetic studies. Two concepts are key to understanding RNA structure: hierarchical organization of global structure and isostericity of local interactions. Global structure changes extremely slowly, as it relies on conserved long-range tertiary interactions. Tertiary RNA–RNA and quaternary RNA–protein interactions are mediated by RNA motifs, defined as recurrent and ordered arrays of non-Watson–Crick base-pairs. A single RNA motif comprises a family of sequences, all of which can fold into the same three-dimensional structure and can mediate the same interaction(s). The chemistry and geometry of base pairing constrain the evolution of motifs in such a way that random mutations that occur within motifs are accepted or rejected insofar as they can mediate a similar ordered array of interactions. The steps involved in the analysis and annotation of RNA motifs in 3D structures are: (a) decomposition of each motif into non-Watson–Crick base-pairs; (b) geometric classification of each basepair; (c) identification of isosteric substitutions for each basepair by comparison to isostericity matrices; (d) alignment of homologous sequences using the isostericity matrices to identify corresponding positions in the crystal structure; (e) acceptance or rejection of the null hypothesis that the motif is conserved.
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spelling pubmed-24484142008-07-14 The Annotation of RNA Motifs Leontis, Neocles B. Westhof, Eric Comp Funct Genomics Research Article The recent deluge of new RNA structures, including complete atomic-resolution views of both subunits of the ribosome, has on the one hand literally overwhelmed our individual abilities to comprehend the diversity of RNA structure, and on the other hand presented us with new opportunities for comprehensive use of RNA sequences for comparative genetic, evolutionary and phylogenetic studies. Two concepts are key to understanding RNA structure: hierarchical organization of global structure and isostericity of local interactions. Global structure changes extremely slowly, as it relies on conserved long-range tertiary interactions. Tertiary RNA–RNA and quaternary RNA–protein interactions are mediated by RNA motifs, defined as recurrent and ordered arrays of non-Watson–Crick base-pairs. A single RNA motif comprises a family of sequences, all of which can fold into the same three-dimensional structure and can mediate the same interaction(s). The chemistry and geometry of base pairing constrain the evolution of motifs in such a way that random mutations that occur within motifs are accepted or rejected insofar as they can mediate a similar ordered array of interactions. The steps involved in the analysis and annotation of RNA motifs in 3D structures are: (a) decomposition of each motif into non-Watson–Crick base-pairs; (b) geometric classification of each basepair; (c) identification of isosteric substitutions for each basepair by comparison to isostericity matrices; (d) alignment of homologous sequences using the isostericity matrices to identify corresponding positions in the crystal structure; (e) acceptance or rejection of the null hypothesis that the motif is conserved. Hindawi Publishing Corporation 2002-12 /pmc/articles/PMC2448414/ /pubmed/18629252 http://dx.doi.org/10.1002/cfg.213 Text en Copyright © 2002 Hindawi Publishing Corporation. http://creativecommons.org/licenses/by/ This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Leontis, Neocles B.
Westhof, Eric
The Annotation of RNA Motifs
title The Annotation of RNA Motifs
title_full The Annotation of RNA Motifs
title_fullStr The Annotation of RNA Motifs
title_full_unstemmed The Annotation of RNA Motifs
title_short The Annotation of RNA Motifs
title_sort annotation of rna motifs
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2448414/
https://www.ncbi.nlm.nih.gov/pubmed/18629252
http://dx.doi.org/10.1002/cfg.213
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