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

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

Research output: Chapter in Book/Report/Conference proceedingChapter

6 Scopus citations

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.

Original languageEnglish (US)
Title of host publicationDNA-Protein Interactions
Subtitle of host publicationPrinciples and Protocols, Third Edition
EditorsTom Moss, Benoit Leblanc
Pages403-437
Number of pages35
DOIs
StatePublished - 2009

Publication series

NameMethods in Molecular Biology
Volume543
ISSN (Print)1064-3745

All Science Journal Classification (ASJC) codes

  • Molecular Biology
  • Genetics

Keywords

  • Kinetics
  • Open complex
  • Phenyl-azide photoactivatible crosslinking agent
  • Phosphate
  • Phosphorothioate
  • Promoter
  • Protein-DNA interaction
  • Pulsed-laser UV irradiations
  • Quench-flow rapid mixing
  • RNA polymerase
  • Structure
  • Transcription initiation

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