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Literature DB >> 25432749

SHAPE analysis of small RNAs and riboswitches.

Greggory M Rice¹, Steven Busan¹, Fethullah Karabiber², Oleg V Favorov³, Kevin M Weeks⁴.

Abstract

We describe structural analysis of small RNAs by SHAPE chemical probing. RNAs are treated with 1-methyl-7-nitroisatoic anhydride, a reagent that detects local nucleotide flexibility; and N-methylisatoic anhydride and 1-methyl-6-nitroisatoic anhydride, reagents which together detect higher-order and noncanonical interactions. Chemical adducts are quantified as stops during reverse transcriptase-mediated primer extension. Probing information can be used to infer conformational changes and ligand binding and to develop highly accurate models of RNA secondary structures.

Entities: Chemical Disease Gene Species

Keywords: Capillary electrophoresis; QuSHAPE; RNA structure; Riboswitch; SHAPE

Mesh：

Substances：

Year: 2014 PMID： 25432749 PMCID： PMC4896901 DOI： 10.1016/B978-0-12-801122-5.00008-8

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

11 in total

1. RNA structure analysis at single nucleotide resolution by selective 2'-hydroxyl acylation and primer extension (SHAPE).

Authors: Edward J Merino; Kevin A Wilkinson; Jennifer L Coughlan; Kevin M Weeks
Journal: J Am Chem Soc Date: 2005-03-30 Impact factor: 15.419

2. A fast-acting reagent for accurate analysis of RNA secondary and tertiary structure by SHAPE chemistry.

Authors: Stefanie A Mortimer; Kevin M Weeks
Journal: J Am Chem Soc Date: 2007-03-17 Impact factor: 15.419

3. QuShape: rapid, accurate, and best-practices quantification of nucleic acid probing information, resolved by capillary electrophoresis.

Authors: Fethullah Karabiber; Jennifer L McGinnis; Oleg V Favorov; Kevin M Weeks
Journal: RNA Date: 2012-11-27 Impact factor: 4.942

4. Accurate SHAPE-directed RNA secondary structure modeling, including pseudoknots.

Authors: Christine E Hajdin; Stanislav Bellaousov; Wayne Huggins; Christopher W Leonard; David H Mathews; Kevin M Weeks
Journal: Proc Natl Acad Sci U S A Date: 2013-03-15 Impact factor: 11.205

5. Selective 2'-hydroxyl acylation analyzed by protection from exoribonuclease (RNase-detected SHAPE) for direct analysis of covalent adducts and of nucleotide flexibility in RNA.

Authors: Kady-Ann Steen; Nathan A Siegfried; Kevin M Weeks
Journal: Nat Protoc Date: 2011-10-06 Impact factor: 13.491

6. The cellular environment stabilizes adenine riboswitch RNA structure.

Authors: Jillian Tyrrell; Jennifer L McGinnis; Kevin M Weeks; Gary J Pielak
Journal: Biochemistry Date: 2013-11-20 Impact factor: 3.162

7. RNAstructure: software for RNA secondary structure prediction and analysis.

Authors: Jessica S Reuter; David H Mathews
Journal: BMC Bioinformatics Date: 2010-03-15 Impact factor: 3.169

8. Validating fragment-based drug discovery for biological RNAs: lead fragments bind and remodel the TPP riboswitch specifically.

Authors: Katherine Deigan Warner; Philip Homan; Kevin M Weeks; Alison G Smith; Chris Abell; Adrian R Ferré-D'Amaré
Journal: Chem Biol Date: 2014-04-24

9. RNA secondary structure modeling at consistent high accuracy using differential SHAPE.

Authors: Greggory M Rice; Christopher W Leonard; Kevin M Weeks
Journal: RNA Date: 2014-04-17 Impact factor: 4.942

10. Safer one-pot synthesis of the 'SHAPE' reagent 1-methyl-7-nitroisatoic anhydride (1m7).

Authors: Rushia Turner; Kinneret Shefer; Manuel Ares
Journal: RNA Date: 2013-10-18 Impact factor: 4.942

10 in total

Review 1. RNA Structural Differentiation: Opportunities with Pattern Recognition.

Authors: Christopher S Eubanks; Amanda E Hargrove
Journal: Biochemistry Date: 2018-12-18 Impact factor: 3.162

Review 2. Decoding mechanisms by which silent codon changes influence protein biogenesis and function.

Authors: Vedrana Bali; Zsuzsanna Bebok
Journal: Int J Biochem Cell Biol Date: 2015-03-26 Impact factor: 5.085

3. Guidelines for SHAPE Reagent Choice and Detection Strategy for RNA Structure Probing Studies.

Authors: Steven Busan; Chase A Weidmann; Arnab Sengupta; Kevin M Weeks
Journal: Biochemistry Date: 2019-05-30 Impact factor: 3.162

4. Transfection of Sclerotinia sclerotiorum with in vitro transcripts of a naturally occurring interspecific recombinant of Sclerotinia sclerotiorum hypovirus 2 significantly reduces virulence of the fungus.

Authors: Shin-Yi Lee Marzano; Houston A Hobbs; Berlin D Nelson; Glen L Hartman; Darin M Eastburn; Nancy K McCoppin; Leslie L Domier
Journal: J Virol Date: 2015-02-18 Impact factor: 5.103

5. ShapeSorter: a fully probabilistic method for detecting conserved RNA structure features supported by SHAPE evidence.

Authors: Volodymyr Tsybulskyi; Irmtraud M Meyer
Journal: Nucleic Acids Res Date: 2022-08-26 Impact factor: 19.160

Review 6. Using RNA Sequence and Structure for the Prediction of Riboswitch Aptamer: A Comprehensive Review of Available Software and Tools.

Authors: Deborah Antunes; Natasha A N Jorge; Ernesto R Caffarena; Fabio Passetti
Journal: Front Genet Date: 2018-01-19 Impact factor: 4.599

Review 10. Large Noncoding RNAs in Bacteria.

Authors: Kimberly A Harris; Ronald R Breaker
Journal: Microbiol Spectr Date: 2018-07