Literature DB >> 19378179

Static and kinetic site-specific protein-DNA photocrosslinking: analysis of bacterial transcription initiation complexes.

Nikolai Naryshkin1, Sergei Druzhinin, Andrei Revyakin, Younggyu Kim, Vladimir Mekler, Richard H Ebright.   

Abstract

Static site-specific protein-DNA photocrosslinking permits identification of protein-DNA interactions within multiprotein-DNA complexes. Kinetic site-specific protein-DNA photocrosslinking - involving rapid-quench-flow mixing and pulsed-laser irradiation - permits elucidation of pathways and kinetics of formation of protein-DNA interactions within multiprotein-DNA complexes. We present detailed protocols for application of static and kinetic site-specific protein-DNA photocrosslinking to bacterial transcription initiation complexes.

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Year:  2009        PMID： 19378179      PMCID： PMC2733221          DOI： 10.1007/978-1-60327-015-1_25

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


  47 in total

Review 1.  RNA polymerase: structural similarities between bacterial RNA polymerase and eukaryotic RNA polymerase II.

Authors:  R H Ebright
Journal:  J Mol Biol       Date:  2000-12-15       Impact factor: 5.469

2.  Structural organization of the RNA polymerase-promoter open complex.

Authors:  N Naryshkin; A Revyakin; Y Kim; V Mekler; R H Ebright
Journal:  Cell       Date:  2000-06-09       Impact factor: 41.582

3.  The orientation of DNA in an archaeal transcription initiation complex.

Authors:  M S Bartlett; M Thomm; E P Geiduschek
Journal:  Nat Struct Biol       Date:  2000-09

4.  Catabolite gene activator protein (CAP) is not an "acidic activating region" transcription activator protein. Negatively charged amino acids of CAP that are solvent-accessible in the CAP-DNA complex play no role in transcription activation at the lac promoter.

Authors:  X Zhang; Y Zhou; Y W Ebright; R H Ebright
Journal:  J Biol Chem       Date:  1992-04-25       Impact factor: 5.157

5.  Electrophoresis of ribonucleic acid on a polyacrylamide gel which contains disulfide cross-linkages.

Authors:  J N Hansen
Journal:  Anal Biochem       Date:  1976-11       Impact factor: 3.365

6.  Crystal structure of the yeast TFIIA/TBP/DNA complex.

Authors:  J H Geiger; S Hahn; S Lee; P B Sigler
Journal:  Science       Date:  1996-05-10       Impact factor: 47.728

7.  Structural modules of the large subunits of RNA polymerase. Introducing archaebacterial and chloroplast split sites in the beta and beta' subunits of Escherichia coli RNA polymerase.

Authors:  K Severinov; A Mustaev; A Kukarin; O Muzzin; I Bass; S A Darst; A Goldfarb
Journal:  J Biol Chem       Date:  1996-11-01       Impact factor: 5.157

8.  Consensus DNA site for the Escherichia coli catabolite gene activator protein (CAP): CAP exhibits a 450-fold higher affinity for the consensus DNA site than for the E. coli lac DNA site.

Authors:  R H Ebright; Y W Ebright; A Gunasekera
Journal:  Nucleic Acids Res       Date:  1989-12-25       Impact factor: 16.971

9.  Topological localization of the human transcription factors IIA, IIB, TATA box-binding protein, and RNA polymerase II-associated protein 30 on a class II promoter.

Authors:  B Coulombe; J Li; J Greenblatt
Journal:  J Biol Chem       Date:  1994-08-05       Impact factor: 5.157

10.  The subunit structure of Saccharomyces cerevisiae transcription factor IIIC probed with a novel photocrosslinking reagent.

Authors:  B Bartholomew; G A Kassavetis; B R Braun; E P Geiduschek
Journal:  EMBO J       Date:  1990-07       Impact factor: 11.598
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  2 in total

1.  Site-specific incorporation of probes into RNA polymerase by unnatural-amino-acid mutagenesis and Staudinger-Bertozzi ligation.

Authors:  Anirban Chakraborty; Abhishek Mazumder; Miaoxin Lin; Adam Hasemeyer; Qumiao Xu; Dongye Wang; Yon W Ebright; Richard H Ebright
Journal:  Methods Mol Biol       Date:  2015

2.  Identification of proximal sites for unwound DNA substrate in Escherichia coli topoisomerase I with oxidative crosslinking.

Authors:  Bokun Cheng; Qingxuan Zhou; Liwei Weng; John D Leszyk; Marc M Greenberg; Yuk-Ching Tse-Dinh
Journal:  FEBS Lett       Date:  2016-12-20       Impact factor: 4.124
  2 in total

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