Open AccessRNA Structure Analysis of Viruses Using SHAPE
Author(s) -
Burrill Cecily P.,
Andino Raul
Publication year - 2013
Publication title -
current protocols in microbiology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.813
H-Index - 35
eISSN - 1934-8533
pISSN - 1934-8525
DOI - 10.1002/9780471729259.mc15h03s30
Subject(s) - primer extension , rna , biology , acylation , primer (cosmetics) , rna extraction , computational biology , biochemistry , chemistry , gene , organic chemistry , catalysis
Abstract Selective 2′ hydroxyl acylation analyzed by primer extension (SHAPE) provides a means to investigate RNA structure with better resolution and higher throughput than has been possible with traditional methods. We present several protocols, which are based on a variety of previously published methods and were adapted and optimized for the analysis of poliovirus RNA in the Andino laboratory. These include methods for nondenaturing RNA extraction, RNA modification and primer extension, and data processing in ShapeFinder. Curr. Protoc. Microbiol . 30:15H.3.1‐15H.3.12. © 2013 by John Wiley & Sons, Inc.