A Tool to Design Bridging Oligos Used to Detect Pseudouridylation Sites on RNA after CMC Treatment

Pseudouridylation is one of the most abundant modifications found in RNAs. To identify the Pseudouridylation sites (Psi) in RNAs, several techniques have been developed, but the most common and robust is the CMC (N-cyclohexyl-N′-(2-morpholinoethyl)carbodiimide) treatment, which consists in the addit...

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Autores principales: Bogard, Baptiste, Tellier, Gilles, Francastel, Claire, Hubé, Florent
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2022
Materias:
Protocol
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9610020/
https://www.ncbi.nlm.nih.gov/pubmed/36287115
http://dx.doi.org/10.3390/ncrna8050063
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author Bogard, Baptiste
Tellier, Gilles
Francastel, Claire
Hubé, Florent
author_facet Bogard, Baptiste
Tellier, Gilles
Francastel, Claire
Hubé, Florent
author_sort Bogard, Baptiste
collection PubMed
description Pseudouridylation is one of the most abundant modifications found in RNAs. To identify the Pseudouridylation sites (Psi) in RNAs, several techniques have been developed, but the most common and robust is the CMC (N-cyclohexyl-N′-(2-morpholinoethyl)carbodiimide) treatment, which consists in the addition of an adduct on Psi that inhibits the reverse transcription. Here, we describe a turnkey method and a tool to design the bridging oligo (DBO), which is somewhat difficult to design. Finally, we propose a trouble-shooting guide to help users.
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spelling pubmed-96100202022-10-28 A Tool to Design Bridging Oligos Used to Detect Pseudouridylation Sites on RNA after CMC Treatment Bogard, Baptiste Tellier, Gilles Francastel, Claire Hubé, Florent Noncoding RNA Protocol Pseudouridylation is one of the most abundant modifications found in RNAs. To identify the Pseudouridylation sites (Psi) in RNAs, several techniques have been developed, but the most common and robust is the CMC (N-cyclohexyl-N′-(2-morpholinoethyl)carbodiimide) treatment, which consists in the addition of an adduct on Psi that inhibits the reverse transcription. Here, we describe a turnkey method and a tool to design the bridging oligo (DBO), which is somewhat difficult to design. Finally, we propose a trouble-shooting guide to help users. MDPI 2022-09-23 /pmc/articles/PMC9610020/ /pubmed/36287115 http://dx.doi.org/10.3390/ncrna8050063 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Protocol
Bogard, Baptiste
Tellier, Gilles
Francastel, Claire
Hubé, Florent
A Tool to Design Bridging Oligos Used to Detect Pseudouridylation Sites on RNA after CMC Treatment
title A Tool to Design Bridging Oligos Used to Detect Pseudouridylation Sites on RNA after CMC Treatment
title_full A Tool to Design Bridging Oligos Used to Detect Pseudouridylation Sites on RNA after CMC Treatment
title_fullStr A Tool to Design Bridging Oligos Used to Detect Pseudouridylation Sites on RNA after CMC Treatment
title_full_unstemmed A Tool to Design Bridging Oligos Used to Detect Pseudouridylation Sites on RNA after CMC Treatment
title_short A Tool to Design Bridging Oligos Used to Detect Pseudouridylation Sites on RNA after CMC Treatment
title_sort tool to design bridging oligos used to detect pseudouridylation sites on rna after cmc treatment
topic Protocol
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9610020/
https://www.ncbi.nlm.nih.gov/pubmed/36287115
http://dx.doi.org/10.3390/ncrna8050063
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