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Revisiting GNRA and UNCG folds: U-turns versus Z-turns in RNA hairpin loops

When thinking about RNA three-dimensional structures, coming across GNRA and UNCG tetraloops is perceived as a boon since their folds have been extensively described. Nevertheless, analyzing loop conformations within RNA and RNP structures led us to uncover several instances of GNRA and UNCG loops t...

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Detalles Bibliográficos
Autores principales: D'Ascenzo, Luigi, Leonarski, Filip, Vicens, Quentin, Auffinger, Pascal
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Cold Spring Harbor Laboratory Press 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5311481/
https://www.ncbi.nlm.nih.gov/pubmed/27999116
http://dx.doi.org/10.1261/rna.059097.116
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author D'Ascenzo, Luigi
Leonarski, Filip
Vicens, Quentin
Auffinger, Pascal
author_facet D'Ascenzo, Luigi
Leonarski, Filip
Vicens, Quentin
Auffinger, Pascal
author_sort D'Ascenzo, Luigi
collection PubMed
description When thinking about RNA three-dimensional structures, coming across GNRA and UNCG tetraloops is perceived as a boon since their folds have been extensively described. Nevertheless, analyzing loop conformations within RNA and RNP structures led us to uncover several instances of GNRA and UNCG loops that do not fold as expected. We noticed that when a GNRA does not assume its “natural” fold, it adopts the one we typically associate with a UNCG sequence. The same folding interconversion may occur for loops with UNCG sequences, for instance within tRNA anticodon loops. Hence, we show that some structured tetranucleotide sequences starting with G or U can adopt either of these folds. The underlying structural basis that defines these two fold types is the mutually exclusive stacking of a backbone oxygen on either the first (in GNRA) or the last nucleobase (in UNCG), generating an oxygen–π contact. We thereby propose to refrain from using sequences to distinguish between loop conformations. Instead, we suggest using descriptors such as U-turn (for “GNRA-type” folds) and a newly described Z-turn (for “UNCG-type” folds). Because tetraloops adopt for the largest part only two (inter)convertible turns, we are better able to interpret from a structural perspective loop interchangeability occurring in ribosomes and viral RNA. In this respect, we propose a general view on the inclination for a given sequence to adopt (or not) a specific fold. We also suggest how long-noncoding RNAs may adopt discrete but transient structures, which are therefore hard to predict.
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spelling pubmed-53114812017-03-01 Revisiting GNRA and UNCG folds: U-turns versus Z-turns in RNA hairpin loops D'Ascenzo, Luigi Leonarski, Filip Vicens, Quentin Auffinger, Pascal RNA Letter to the Editor When thinking about RNA three-dimensional structures, coming across GNRA and UNCG tetraloops is perceived as a boon since their folds have been extensively described. Nevertheless, analyzing loop conformations within RNA and RNP structures led us to uncover several instances of GNRA and UNCG loops that do not fold as expected. We noticed that when a GNRA does not assume its “natural” fold, it adopts the one we typically associate with a UNCG sequence. The same folding interconversion may occur for loops with UNCG sequences, for instance within tRNA anticodon loops. Hence, we show that some structured tetranucleotide sequences starting with G or U can adopt either of these folds. The underlying structural basis that defines these two fold types is the mutually exclusive stacking of a backbone oxygen on either the first (in GNRA) or the last nucleobase (in UNCG), generating an oxygen–π contact. We thereby propose to refrain from using sequences to distinguish between loop conformations. Instead, we suggest using descriptors such as U-turn (for “GNRA-type” folds) and a newly described Z-turn (for “UNCG-type” folds). Because tetraloops adopt for the largest part only two (inter)convertible turns, we are better able to interpret from a structural perspective loop interchangeability occurring in ribosomes and viral RNA. In this respect, we propose a general view on the inclination for a given sequence to adopt (or not) a specific fold. We also suggest how long-noncoding RNAs may adopt discrete but transient structures, which are therefore hard to predict. Cold Spring Harbor Laboratory Press 2017-03 /pmc/articles/PMC5311481/ /pubmed/27999116 http://dx.doi.org/10.1261/rna.059097.116 Text en © 2017 D'Ascenzo et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society http://creativecommons.org/licenses/by/4.0/ This article, published in RNA, is available under a Creative Commons License (Attribution 4.0 International), as described at http://creativecommons.org/licenses/by/4.0/.
spellingShingle Letter to the Editor
D'Ascenzo, Luigi
Leonarski, Filip
Vicens, Quentin
Auffinger, Pascal
Revisiting GNRA and UNCG folds: U-turns versus Z-turns in RNA hairpin loops
title Revisiting GNRA and UNCG folds: U-turns versus Z-turns in RNA hairpin loops
title_full Revisiting GNRA and UNCG folds: U-turns versus Z-turns in RNA hairpin loops
title_fullStr Revisiting GNRA and UNCG folds: U-turns versus Z-turns in RNA hairpin loops
title_full_unstemmed Revisiting GNRA and UNCG folds: U-turns versus Z-turns in RNA hairpin loops
title_short Revisiting GNRA and UNCG folds: U-turns versus Z-turns in RNA hairpin loops
title_sort revisiting gnra and uncg folds: u-turns versus z-turns in rna hairpin loops
topic Letter to the Editor
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5311481/
https://www.ncbi.nlm.nih.gov/pubmed/27999116
http://dx.doi.org/10.1261/rna.059097.116
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