Literature DB >> 20946769

Chemical probing of RNA and RNA/protein complexes.

Zhili Xu1, Gloria M Culver.   

Abstract

Chemical probing is widely used as a rapid approach for assessing RNA structure, folding, and function. In this chapter, we outline procedures for handling and using chemicals commonly used to probe nucleic acids. Detailed experimental conditions and design for footprinting and modification interference are presented herein. Protocols for RNA extraction, normalization, primer extension, and data evaluation are also provided. The methods described are designed to aid in the study of large RNAs, but with slight modifications are applicable to smaller RNAs.
Copyright © 2009 Elsevier Inc. All rights reserved.

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Year:  2009        PMID： 20946769     DOI： 10.1016/S0076-6879(09)68008-3

Source DB:  PubMed          Journal:  Methods Enzymol        ISSN： 0076-6879            Impact factor:   1.600


  10 in total

1.  Differential assembly of 16S rRNA domains during 30S subunit formation.

Authors:  Zhili Xu; Gloria M Culver
Journal:  RNA       Date:  2010-08-24       Impact factor: 4.942

2.  Saccharomyces cerevisiae ribosomal protein L26 is not essential for ribosome assembly and function.

Authors:  Reyes Babiano; Michael Gamalinda; John L Woolford; Jesús de la Cruz
Journal:  Mol Cell Biol       Date:  2012-06-11       Impact factor: 4.272

3.  A trans-spliced telomerase RNA dictates telomere synthesis in Trypanosoma brucei.

Authors:  Ranjodh Sandhu; Samantha Sanford; Shrabani Basu; Mina Park; Unnati M Pandya; Bibo Li; Kausik Chakrabarti
Journal:  Cell Res       Date:  2013-03-12       Impact factor: 25.617

4.  Mechanistic studies of non-canonical amino acid mutagenesis.

Authors:  Rachel C Fleisher; Nina Michael; Ruben L Gonzalez
Journal:  Methods Enzymol       Date:  2021-06-24       Impact factor: 1.682

5.  The SBP2 protein central to selenoprotein synthesis contacts the human ribosome at expansion segment 7L of the 28S rRNA.

Authors:  Olga Kossinova; Alexey Malygin; Alain Krol; Galina Karpova
Journal:  RNA       Date:  2014-05-21       Impact factor: 4.942

6.  Understanding in-line probing experiments by modeling cleavage of nonreactive RNA nucleotides.

Authors:  Vojtěch Mlýnský; Giovanni Bussi
Journal:  RNA       Date:  2017-02-15       Impact factor: 4.942

7.  Keth-seq for transcriptome-wide RNA structure mapping.

Authors:  Xiaocheng Weng; Jing Gong; Yi Chen; Tong Wu; Fang Wang; Shixi Yang; Yushu Yuan; Guanzheng Luo; Kai Chen; Lulu Hu; Honghui Ma; Pingluan Wang; Qiangfeng Cliff Zhang; Xiang Zhou; Chuan He
Journal:  Nat Chem Biol       Date:  2020-02-03       Impact factor: 15.040

8.  SHAPE Profiling to Probe Group II Intron Conformational Dynamics During Splicing.

Authors:  Timothy Wiryaman; Navtej Toor
Journal:  Methods Mol Biol       Date:  2021

9.  Yeast polypeptide exit tunnel ribosomal proteins L17, L35 and L37 are necessary to recruit late-assembling factors required for 27SB pre-rRNA processing.

Authors:  Michael Gamalinda; Jelena Jakovljevic; Reyes Babiano; Jason Talkish; Jesús de la Cruz; John L Woolford
Journal:  Nucleic Acids Res       Date:  2012-12-24       Impact factor: 16.971

10.  Multiple in vivo pathways for Escherichia coli small ribosomal subunit assembly occur on one pre-rRNA.

Authors:  Neha Gupta; Gloria M Culver
Journal:  Nat Struct Mol Biol       Date:  2014-09-07       Impact factor: 15.369
  10 in total

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