title: Using solutes and kinetics to probe large conformational changes in the steps of transcription initiation.
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.
authors: Department of Chemistry, 3206 BSB, University of Wisconsin-Madison, Madison, WI, 53706, USA, eruff@chem.wisc.edu.
authors: Emily F
authors: EF
authors: Ruff
authors: Wayne S
authors: WS
authors: Kontur
authors: M Thomas
authors: MT
authors: Record
mesh_terms: D003101:Collodion; D012321:DNA-Directed RNA Polymerases / Q000378:metabolism*; D004926:Escherichia coli / Q000201:enzymology* / Q000502:physiology; D007700:Kinetics; D015335:Molecular Probes / Q000378:metabolism*; D011487:Protein Conformation; D061785:Transcription Initiation, Genetic / Q000502:physiology*
chemical_list: D015335:Molecular Probes; D003101:Collodion; D012321:DNA-Directed RNA Polymerases