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Drennan, Amanda; Kraemer, Mark; Capp, Michael et al. (2012) Key roles of the downstream mobile jaw of Escherichia coli RNA polymerase in transcription initiation. Biochemistry 51:9447-59
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Saecker, Ruth M; Record Jr, M Thomas; Dehaseth, Pieter L (2011) Mechanism of bacterial transcription initiation: RNA polymerase - promoter binding, isomerization to initiation-competent open complexes, and initiation of RNA synthesis. J Mol Biol 412:754-71
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Koh, Junseock; Shkel, Irina; Saecker, Ruth M et al. (2011) Nonspecific DNA binding and bending by HU??: interfaces of the three binding modes characterized by salt-dependent thermodynamics. J Mol Biol 410:241-67
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Kontur, Wayne S; Capp, Michael W; Gries, Theodore J et al. (2010) Probing DNA binding, DNA opening, and assembly of a downstream clamp/jaw in Escherichia coli RNA polymerase-lambdaP(R) promoter complexes using salt and the physiological anion glutamate. Biochemistry 49:4361-73
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Gries, Theodore J; Kontur, Wayne S; Capp, Michael W et al. (2010) One-step DNA melting in the RNA polymerase cleft opens the initiation bubble to form an unstable open complex. Proc Natl Acad Sci U S A 107:10418-23
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Capp, Michael W; Pegram, Laurel M; Saecker, Ruth M et al. (2009) Interactions of the osmolyte glycine betaine with molecular surfaces in water: thermodynamics, structural interpretation, and prediction of m-values. Biochemistry 48:10372-9
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Schroeder, Lisa A; Gries, Theodore J; Saecker, Ruth M et al. (2009) Evidence for a tyrosine-adenine stacking interaction and for a short-lived open intermediate subsequent to initial binding of Escherichia coli RNA polymerase to promoter DNA. J Mol Biol 385:339-49
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Pegram, Laurel M; Record Jr, M Thomas (2009) Quantifying the roles of water and solutes (denaturants, osmolytes, and Hofmeister salts) in protein and model processes using the solute partitioning model. Methods Mol Biol 490:179-93
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Vander Meulen, Kirk A; Saecker, Ruth M; Record Jr, M Thomas (2008) Formation of a wrapped DNA-protein interface: experimental characterization and analysis of the large contributions of ions and water to the thermodynamics of binding IHF to H'DNA. J Mol Biol 377:9-27
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Kontur, Wayne S; Saecker, Ruth M; Capp, Michael W et al. (2008) Late steps in the formation of E. coli RNA polymerase-lambda P R promoter open complexes: characterization of conformational changes by rapid [perturbant] upshift experiments. J Mol Biol 376:1034-47
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