Literature DB >> 18428862

Probing RNA structure with chemical reagents and enzymes.

W A Ziehler1, D R Engelke.   

Abstract

This unit provides thorough coverage of the most useful chemical and enzyme probes that can be used to examine RNA secondary and tertiary structure. Footprinting methods are presented using dimethyl sulfate, diethyl pyrocarbonate, ethylnitrosourea, kethoxal, CMCT, and nucleases. For chemical probes, both strand scission and primer extension detection protocols are included.

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Year:  2001        PMID： 18428862      PMCID： PMC3746551          DOI： 10.1002/0471142700.nc0601s00

Source DB:  PubMed          Journal:  Curr Protoc Nucleic Acid Chem        ISSN： 1934-9270


  10 in total

1.  Computer modeling and display of RNA secondary and tertiary structures.

Authors:  D Gautheret; F Major; R Cedergren
Journal:  Methods Enzymol       Date:  1990       Impact factor: 1.600

2.  The combination of symbolic and numerical computation for three-dimensional modeling of RNA.

Authors:  F Major; M Turcotte; D Gautheret; G Lapalme; E Fillion; R Cedergren
Journal:  Science       Date:  1991-09-13       Impact factor: 47.728

3.  Coaxial stacking of helixes enhances binding of oligoribonucleotides and improves predictions of RNA folding.

Authors:  A E Walter; D H Turner; J Kim; M H Lyttle; P Müller; D H Mathews; M Zuker
Journal:  Proc Natl Acad Sci U S A       Date:  1994-09-27       Impact factor: 11.205

4.  Finding the most significant common sequence and structure motifs in a set of RNA sequences.

Authors:  J Gorodkin; L J Heyer; G D Stormo
Journal:  Nucleic Acids Res       Date:  1997-09-15       Impact factor: 16.971

5.  Synthesis of small RNAs using T7 RNA polymerase.

Authors:  J F Milligan; O C Uhlenbeck
Journal:  Methods Enzymol       Date:  1989       Impact factor: 1.600

6.  A guide for probing native small nuclear RNA and ribonucleoprotein structures.

Authors:  A Krol; P Carbon
Journal:  Methods Enzymol       Date:  1989       Impact factor: 1.600

Review 7.  On finding all suboptimal foldings of an RNA molecule.

Authors:  M Zuker
Journal:  Science       Date:  1989-04-07       Impact factor: 47.728

8.  Specific labeling of 3' termini of RNA with T4 RNA ligase.

Authors:  T E England; A G Bruce; O C Uhlenbeck
Journal:  Methods Enzymol       Date:  1980       Impact factor: 1.600

9.  Chemical probes for higher-order structure in RNA.

Authors:  D A Peattie; W Gilbert
Journal:  Proc Natl Acad Sci U S A       Date:  1980-08       Impact factor: 11.205

10.  Enzymatic approaches to probing of RNA secondary and tertiary structure.

Authors:  G Knapp
Journal:  Methods Enzymol       Date:  1989       Impact factor: 1.600
  10 in total
  38 in total

1.  Probing-directed identification of novel structured RNAs.

Authors:  Svetlana V Vinogradova; Roman A Sutormin; Andrey A Mironov; Ruslan A Soldatov
Journal:  RNA Biol       Date:  2016       Impact factor: 4.652

Review 2.  Probing dimensionality beyond the linear sequence of mRNA.

Authors:  Cristian Del Campo; Zoya Ignatova
Journal:  Curr Genet       Date:  2015-12-09       Impact factor: 3.886

3.  Differentiation and classification of RNA motifs using small molecule-based pattern recognition.

Authors:  Giacomo Padroni; Christopher S Eubanks; Amanda E Hargrove
Journal:  Methods Enzymol       Date:  2019-06-13       Impact factor: 1.600

4.  Identification of N6-methyladenosine reader proteins.

Authors:  Katherine I Zhou; Nian Liu; Tao Pan
Journal:  Methods       Date:  2017-04-26       Impact factor: 3.608

Review 5.  Insights into RNA structure and function from genome-wide studies.

Authors:  Stefanie A Mortimer; Mary Anne Kidwell; Jennifer A Doudna
Journal:  Nat Rev Genet       Date:  2014-05-13       Impact factor: 53.242

Review 6.  Computational analysis of RNA structures with chemical probing data.

Authors:  Ping Ge; Shaojie Zhang
Journal:  Methods       Date:  2015-02-14       Impact factor: 3.608

7.  Interpreting Reverse Transcriptase Termination and Mutation Events for Greater Insight into the Chemical Probing of RNA.

Authors:  Alec N Sexton; Peter Y Wang; Michael Rutenberg-Schoenberg; Matthew D Simon
Journal:  Biochemistry       Date:  2017-08-18       Impact factor: 3.162

Review 8.  Progress and challenges for chemical probing of RNA structure inside living cells.

Authors:  Miles Kubota; Catherine Tran; Robert C Spitale
Journal:  Nat Chem Biol       Date:  2015-11-17       Impact factor: 15.040

9.  Structural basis for the methylation of G1405 in 16S rRNA by aminoglycoside resistance methyltransferase Sgm from an antibiotic producer: a diversity of active sites in m7G methyltransferases.

Authors:  Nilofer Husain; Karolina L Tkaczuk; Shenoy Rajesh Tulsidas; Katarzyna H Kaminska; Sonja Cubrilo; Gordana Maravić-Vlahovicek; Janusz M Bujnicki; J Sivaraman
Journal:  Nucleic Acids Res       Date:  2010-03-01       Impact factor: 16.971

10.  Comparisons between chemical mapping and binding to isoenergetic oligonucleotide microarrays reveal unexpected patterns of binding to the Bacillus subtilis RNase P RNA specificity domain.

Authors:  Ruiting Liang; Elzbieta Kierzek; Ryszard Kierzek; Douglas H Turner
Journal:  Biochemistry       Date:  2010-09-21       Impact factor: 3.162
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