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On the role of four small hairpins in the HIV-1 RNA genome

An RNA secondary structure model for the complete HIV-1 genome has recently been published based on SHAPE technology. Several well-known RNA motifs such as TAR and RRE were confirmed and numerous new structured motifs were described that may play important roles in virus replication. The 9 kb viral...

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Autores principales: Knoepfel, Stefanie A., Berkhout, Ben
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Landes Bioscience 2013
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3710360/
https://www.ncbi.nlm.nih.gov/pubmed/23535706
http://dx.doi.org/10.4161/rna.24133
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author Knoepfel, Stefanie A.
Berkhout, Ben
author_facet Knoepfel, Stefanie A.
Berkhout, Ben
author_sort Knoepfel, Stefanie A.
collection PubMed
description An RNA secondary structure model for the complete HIV-1 genome has recently been published based on SHAPE technology. Several well-known RNA motifs such as TAR and RRE were confirmed and numerous new structured motifs were described that may play important roles in virus replication. The 9 kb viral RNA genome is densely packed with many RNA hairpin motifs and the collective fold may play an important role in HIV-1 biology. We initially focused on 16 RNA hairpin motifs scattered along the viral genome. We considered conservation of these structures, despite sequence variation among virus isolates, as a first indication for a significant function. Four relatively small hairpins exhibited considerable structural conservation and were selected for experimental validation in virus replication assays. Mutations were introduced into the HIV-1 RNA genome to destabilize individual RNA structures without affecting the protein-coding properties (silent codon changes). No major virus replication defects were scored, suggesting that these four hairpin structures do not play essential roles in HIV-1 replication.
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spelling pubmed-37103602013-07-25 On the role of four small hairpins in the HIV-1 RNA genome Knoepfel, Stefanie A. Berkhout, Ben RNA Biol Research Paper An RNA secondary structure model for the complete HIV-1 genome has recently been published based on SHAPE technology. Several well-known RNA motifs such as TAR and RRE were confirmed and numerous new structured motifs were described that may play important roles in virus replication. The 9 kb viral RNA genome is densely packed with many RNA hairpin motifs and the collective fold may play an important role in HIV-1 biology. We initially focused on 16 RNA hairpin motifs scattered along the viral genome. We considered conservation of these structures, despite sequence variation among virus isolates, as a first indication for a significant function. Four relatively small hairpins exhibited considerable structural conservation and were selected for experimental validation in virus replication assays. Mutations were introduced into the HIV-1 RNA genome to destabilize individual RNA structures without affecting the protein-coding properties (silent codon changes). No major virus replication defects were scored, suggesting that these four hairpin structures do not play essential roles in HIV-1 replication. Landes Bioscience 2013-04-01 2013-03-27 /pmc/articles/PMC3710360/ /pubmed/23535706 http://dx.doi.org/10.4161/rna.24133 Text en Copyright © 2013 Landes Bioscience http://creativecommons.org/licenses/by-nc/3.0/ This is an open-access article licensed under a Creative Commons Attribution-NonCommercial 3.0 Unported License. The article may be redistributed, reproduced, and reused for non-commercial purposes, provided the original source is properly cited.
spellingShingle Research Paper
Knoepfel, Stefanie A.
Berkhout, Ben
On the role of four small hairpins in the HIV-1 RNA genome
title On the role of four small hairpins in the HIV-1 RNA genome
title_full On the role of four small hairpins in the HIV-1 RNA genome
title_fullStr On the role of four small hairpins in the HIV-1 RNA genome
title_full_unstemmed On the role of four small hairpins in the HIV-1 RNA genome
title_short On the role of four small hairpins in the HIV-1 RNA genome
title_sort on the role of four small hairpins in the hiv-1 rna genome
topic Research Paper
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3710360/
https://www.ncbi.nlm.nih.gov/pubmed/23535706
http://dx.doi.org/10.4161/rna.24133
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