Document Type

Article

Publication Version

Published Version

Publication Date

1-2015

Journal or Book Title

bio-protocol

Volume

5

Issue

2

First Page

e1386-1

Last Page

e1386-9

Abstract

This protocol describes the methodology for the determination of the secondary structure of an RNA fragment in solution using Selective 2´-Hydroxyl Acylation analyzed by Primer Extension, abbreviation SHAPE. It consists in the very fast chemical modification of flexible and therefore possibly single-stranded nucleotides in a sequence-independent manner using benzoyl cyanide (BzCN), forming 2´-O-adducts. The modifications in the RNA are then analyzed by primer extension. Reverse transcriptase is blocked by the 2´-O-adducts formed. The advantage of the method is, first, that not each RNA molecule studied but the primer used in the extension reaction is labelled and, second, that the resulting cDNA analyzed in sequencing gels is much more stable than the modified RNA

Comments

This article is from Bio-protocol 5 (2015): e1386. Posted with permission.

Rights

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.

Copyright Owner

Bio-protocol LLC

Language

en

File Format

application/pdf

Published Version

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