Using solutes and kinetics to probe large conformational changes in the steps of transcription initiation

Emily F. Ruff, Wayne S. Kontur, M. Thomas Record

Research output: Contribution to journalArticlepeer-review

Abstract

Small solutes are useful probes of large conformational changes in RNA polymerase–promoter interactions and other biopolymer processes. In general, a large effect of a solute on an equilibrium constant (or rate constant) indicates a large change in water-accessible biopolymer surface area in the corresponding step (or transition state), resulting from conformational changes, interface formation, or both. Here, we describe nitrocellulose filter binding assays from series used to determine the urea dependence of open complex formation and dissociation with Escherichia coli RNA polymerase and phage λPR promoter DNA. Then, we describe the subsequent data analysis and interpretation of these solute effects.

Original languageEnglish (US)
Pages (from-to)241-261
Number of pages21
JournalMethods in Molecular Biology
Volume1276
DOIs
StatePublished - Jan 1 2015

Keywords

  • Conformational changes
  • Kinetics
  • Mechanism
  • Open complex formation
  • RNA polymerase
  • Solute effects

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