Literature DB >> 18982286

Quantitative analysis of protein-RNA interactions by gel mobility shift.

Sean P Ryder1, Michael I Recht, James R Williamson.   

Abstract

The gel mobility shift assay is routinely used to visualize protein-RNA interactions. Its power resides in the ability to resolve free from bound RNA with high resolution in a gel matrix. We review the quantitative application of this approach to elucidate thermodynamic properties of protein-RNA complexes. Assay designs for titration, competition, and stoichiometry experiments are presented for two unrelated model complexes.

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Year:  2008        PMID： 18982286      PMCID： PMC2928675          DOI： 10.1007/978-1-60327-475-3_7

Source DB:  PubMed          Journal:  Methods Mol Biol        ISSN： 1064-3745


  18 in total

1.  Measuring equilibrium and kinetic constants using gel retardation assays.

Authors:  D R Setzer
Journal:  Methods Mol Biol       Date:  1999

2.  Central domain assembly: thermodynamics and kinetics of S6 and S18 binding to an S15-RNA complex.

Authors:  M I Recht; J R Williamson
Journal:  J Mol Biol       Date:  2001-10-12       Impact factor: 5.469

3.  RNA target specificity of the STAR/GSG domain post-transcriptional regulatory protein GLD-1.

Authors:  Sean P Ryder; Leah A Frater; Dana L Abramovitz; Elizabeth B Goodwin; James R Williamson
Journal:  Nat Struct Mol Biol       Date:  2003-12-29       Impact factor: 15.369

4.  Phenomenological theory of gel electrophoresis of protein-nucleic acid complexes.

Authors:  J R Cann
Journal:  J Biol Chem       Date:  1989-10-15       Impact factor: 5.157

5.  Lac repressor binding to non-operator DNA: detailed studies and a comparison of eequilibrium and rate competition methods.

Authors:  S Y Lin; A D Riggs
Journal:  J Mol Biol       Date:  1972-12-30       Impact factor: 5.469

6.  Molecular interactions of ribosomal components. I. Identification of RNA binding sites for individual 30S ribosomal proteins.

Authors:  H W Schaup; M Green; C G Kurland
Journal:  Mol Gen Genet       Date:  1970

7.  Electrophoretic characterization of bacterial polyribosomes in agarose-acrylamide composite gels.

Authors:  A E Dahlberg; C W Dingman; A C Peacock
Journal:  J Mol Biol       Date:  1969-04-14       Impact factor: 5.469

8.  Effects of mutations in the L-tryptophan binding pocket of the Trp RNA-binding attenuation protein of Bacillus subtilis.

Authors:  A V Yakhnin; J J Trimble; C R Chiaro; P Babitzke
Journal:  J Biol Chem       Date:  2000-02-11       Impact factor: 5.157

9.  The Pumilio protein binds RNA through a conserved domain that defines a new class of RNA-binding proteins.

Authors:  P D Zamore; J R Williamson; R Lehmann
Journal:  RNA       Date:  1997-12       Impact factor: 4.942

10.  Size selective recognition of siRNA by an RNA silencing suppressor.

Authors:  Jeffrey M Vargason; György Szittya; József Burgyán; Traci M Tanka Hall
Journal:  Cell       Date:  2003-12-26       Impact factor: 41.582
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  93 in total

1.  Visualization and genetic analysis of alternative splicing regulation in vivo using fluorescence reporters in transgenic Caenorhabditis elegans.

Authors:  Hidehito Kuroyanagi; Genta Ohno; Hiroaki Sakane; Hiroyuki Maruoka; Masatoshi Hagiwara
Journal:  Nat Protoc       Date:  2010-08-05       Impact factor: 13.491

2.  Preparation of cooperative RNA recognition complexes for crystallographic structural studies.

Authors:  Chen Qiu; Aaron C Goldstrohm; Traci M Tanaka Hall
Journal:  Methods Enzymol       Date:  2019-05-02       Impact factor: 1.600

Review 3.  Quantitative approaches to monitor protein-nucleic acid interactions using fluorescent probes.

Authors:  John M Pagano; Carina C Clingman; Sean P Ryder
Journal:  RNA       Date:  2010-11-22       Impact factor: 4.942

Review 4.  mRNA on the move: the road to its biological destiny.

Authors:  Carolina Eliscovich; Adina R Buxbaum; Zachary B Katz; Robert H Singer
Journal:  J Biol Chem       Date:  2013-05-28       Impact factor: 5.157

5.  Human T-cell leukemia virus type 1 Gag domains have distinct RNA-binding specificities with implications for RNA packaging and dimerization.

Authors:  Weixin Wu; Joshua Hatterschide; Yu-Ci Syu; William A Cantara; Ruth J Blower; Heather M Hanson; Louis M Mansky; Karin Musier-Forsyth
Journal:  J Biol Chem       Date:  2018-09-14       Impact factor: 5.157

Review 6.  Approaches for measuring the dynamics of RNA-protein interactions.

Authors:  Donny D Licatalosi; Xuan Ye; Eckhard Jankowsky
Journal:  Wiley Interdiscip Rev RNA       Date:  2019-08-20       Impact factor: 9.957

7.  The N-terminal peptide of the syntaxin Tlg2p modulates binding of its closed conformation to Vps45p.

Authors:  Melonnie L M Furgason; Chris MacDonald; Scott G Shanks; Sean P Ryder; Nia J Bryant; Mary Munson
Journal:  Proc Natl Acad Sci U S A       Date:  2009-08-10       Impact factor: 11.205

8.  Translation inhibition from a distance: The small RNA SgrS silences a ribosomal protein S1-dependent enhancer.

Authors:  Muhammad S Azam; Carin K Vanderpool
Journal:  Mol Microbiol       Date:  2020-05-02       Impact factor: 3.501

9.  ZBP1 recognition of beta-actin zipcode induces RNA looping.

Authors:  Jeffrey A Chao; Yury Patskovsky; Vivek Patel; Matthew Levy; Steven C Almo; Robert H Singer
Journal:  Genes Dev       Date:  2010-01-15       Impact factor: 11.361

10.  Pervasive Regulatory Functions of mRNA Structure Revealed by High-Resolution SHAPE Probing.

Authors:  Anthony M Mustoe; Steven Busan; Greggory M Rice; Christine E Hajdin; Brant K Peterson; Vera M Ruda; Neil Kubica; Razvan Nutiu; Jeremy L Baryza; Kevin M Weeks
Journal:  Cell       Date:  2018-03-15       Impact factor: 41.582
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