In Vitro Methods to Decipher the Structure of Viral RNA Genomes

RNA viruses encode essential information in their genomes as conserved structural elements that are involved in efficient viral protein synthesis, replication, and encapsidation. These elements can also establish complex networks of RNA-RNA interactions, the so-called RNA interactome, to shape the v...

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Autores principales:	Cristina Romero-López, Sara Esther Ramos-Lorente, Alfredo Berzal-Herranz
Formato:	article
Lenguaje:	EN
Publicado:	MDPI AG 2021
Materias:	RNA structure interactome RNA probing long-distant RNA-RNA interactions molecular interference SHAPE Medicine R Pharmacy and materia medica RS1-441
Acceso en línea:	https://doaj.org/article/bb5a0c706ea548a98f6b8e1a5df13f05
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spelling	oai:doaj.org-article:bb5a0c706ea548a98f6b8e1a5df13f052021-11-25T18:40:05ZIn Vitro Methods to Decipher the Structure of Viral RNA Genomes10.3390/ph141111921424-8247https://doaj.org/article/bb5a0c706ea548a98f6b8e1a5df13f052021-11-01T00:00:00Zhttps://www.mdpi.com/1424-8247/14/11/1192https://doaj.org/toc/1424-8247RNA viruses encode essential information in their genomes as conserved structural elements that are involved in efficient viral protein synthesis, replication, and encapsidation. These elements can also establish complex networks of RNA-RNA interactions, the so-called RNA interactome, to shape the viral genome and control different events during intracellular infection. In recent years, targeting these conserved structural elements has become a promising strategy for the development of new antiviral tools due to their sequence and structural conservation. In this context, RNA-based specific therapeutic strategies, such as the use of siRNAs have been extensively pursued to target the genome of different viruses. Importantly, siRNA-mediated targeting is not a straightforward approach and its efficiency is highly dependent on the structure of the target region. Therefore, the knowledge of the viral structure is critical for the identification of potentially good target sites. Here, we describe detailed protocols used in our laboratory for the in vitro study of the structure of viral RNA genomes. These protocols include DMS (dimethylsulfate) probing, SHAPE (selective 2′-hydroxyl acylation analyzed by primer extension) analysis, and HMX (2′-hydroxyl molecular interference). These methodologies involve the use of high-throughput analysis techniques that provide extensive information about the 3D folding of the RNA under study and the structural tuning derived from the interactome activity. They are therefore a good tool for the development of new RNA-based antiviral compounds.Cristina Romero-LópezSara Esther Ramos-LorenteAlfredo Berzal-HerranzMDPI AGarticleRNA structureinteractomeRNA probinglong-distant RNA-RNA interactionsmolecular interferenceSHAPEMedicineRPharmacy and materia medicaRS1-441ENPharmaceuticals, Vol 14, Iss 1192, p 1192 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	RNA structure interactome RNA probing long-distant RNA-RNA interactions molecular interference SHAPE Medicine R Pharmacy and materia medica RS1-441
spellingShingle	RNA structure interactome RNA probing long-distant RNA-RNA interactions molecular interference SHAPE Medicine R Pharmacy and materia medica RS1-441 Cristina Romero-López Sara Esther Ramos-Lorente Alfredo Berzal-Herranz In Vitro Methods to Decipher the Structure of Viral RNA Genomes
description	RNA viruses encode essential information in their genomes as conserved structural elements that are involved in efficient viral protein synthesis, replication, and encapsidation. These elements can also establish complex networks of RNA-RNA interactions, the so-called RNA interactome, to shape the viral genome and control different events during intracellular infection. In recent years, targeting these conserved structural elements has become a promising strategy for the development of new antiviral tools due to their sequence and structural conservation. In this context, RNA-based specific therapeutic strategies, such as the use of siRNAs have been extensively pursued to target the genome of different viruses. Importantly, siRNA-mediated targeting is not a straightforward approach and its efficiency is highly dependent on the structure of the target region. Therefore, the knowledge of the viral structure is critical for the identification of potentially good target sites. Here, we describe detailed protocols used in our laboratory for the in vitro study of the structure of viral RNA genomes. These protocols include DMS (dimethylsulfate) probing, SHAPE (selective 2′-hydroxyl acylation analyzed by primer extension) analysis, and HMX (2′-hydroxyl molecular interference). These methodologies involve the use of high-throughput analysis techniques that provide extensive information about the 3D folding of the RNA under study and the structural tuning derived from the interactome activity. They are therefore a good tool for the development of new RNA-based antiviral compounds.
format	article
author	Cristina Romero-López Sara Esther Ramos-Lorente Alfredo Berzal-Herranz
author_facet	Cristina Romero-López Sara Esther Ramos-Lorente Alfredo Berzal-Herranz
author_sort	Cristina Romero-López
title	In Vitro Methods to Decipher the Structure of Viral RNA Genomes
title_short	In Vitro Methods to Decipher the Structure of Viral RNA Genomes
title_full	In Vitro Methods to Decipher the Structure of Viral RNA Genomes
title_fullStr	In Vitro Methods to Decipher the Structure of Viral RNA Genomes
title_full_unstemmed	In Vitro Methods to Decipher the Structure of Viral RNA Genomes
title_sort	in vitro methods to decipher the structure of viral rna genomes
publisher	MDPI AG
publishDate	2021
url	https://doaj.org/article/bb5a0c706ea548a98f6b8e1a5df13f05
work_keys_str_mv	AT cristinaromerolopez invitromethodstodecipherthestructureofviralrnagenomes AT saraestherramoslorente invitromethodstodecipherthestructureofviralrnagenomes AT alfredoberzalherranz invitromethodstodecipherthestructureofviralrnagenomes
_version_	1718410860846645248

In Vitro Methods to Decipher the Structure of Viral RNA Genomes

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