Humana Press, Methods in Molecular Biology, p. 241-261, 2015
DOI: 10.1007/978-1-4939-2392-2_14
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Small solutes are useful probes of large conformational changes in RNA polymerase (RNAP)-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 RNAP and λPR promoter DNA. Then, we describe the subsequent data analysis and interpretation of these solute effects.