Published in Proc Natl Acad Sci U S A on December 30, 2004
Advances in bacterial promoter recognition and its control by factors that do not bind DNA. Nat Rev Microbiol (2008) 3.05
Mechanism of bacterial transcription initiation: RNA polymerase - promoter binding, isomerization to initiation-competent open complexes, and initiation of RNA synthesis. J Mol Biol (2011) 2.50
Transcription initiation by mix and match elements: flexibility for polymerase binding to bacterial promoters. Gene Regul Syst Bio (2007) 1.58
Sequence-independent upstream DNA-alphaCTD interactions strongly stimulate Escherichia coli RNA polymerase-lacUV5 promoter association. Proc Natl Acad Sci U S A (2004) 1.52
Real-time footprinting of DNA in the first kinetically significant intermediate in open complex formation by Escherichia coli RNA polymerase. Proc Natl Acad Sci U S A (2007) 1.44
Real-time characterization of intermediates in the pathway to open complex formation by Escherichia coli RNA polymerase at the T7A1 promoter. Proc Natl Acad Sci U S A (2005) 1.36
Identification of multiple rate-limiting steps during the human mitochondrial transcription cycle in vitro. J Biol Chem (2010) 1.09
Analysis of RNA polymerase-promoter complex formation. Methods (2008) 1.08
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 (2010) 1.07
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 (2010) 1.05
Initial events in bacterial transcription initiation. Biomolecules (2015) 1.04
Predicting the strength of UP-elements and full-length E. coli σE promoters. Nucleic Acids Res (2011) 0.95
DNA melting by RNA polymerase at the T7A1 promoter precedes the rate-limiting step at 37 degrees C and results in the accumulation of an off-pathway intermediate. Nucleic Acids Res (2009) 0.94
Upstream promoter sequences and alphaCTD mediate stable DNA wrapping within the RNA polymerase-promoter open complex. EMBO Rep (2007) 0.92
General transfer matrix formalism to calculate DNA-protein-drug binding in gene regulation: application to OR operator of phage lambda. Nucleic Acids Res (2007) 0.90
Key roles of the downstream mobile jaw of Escherichia coli RNA polymerase in transcription initiation. Biochemistry (2012) 0.90
RNA polymerase and an activator form discrete subcomplexes in a transcription initiation complex. EMBO J (2006) 0.89
Structural modules of RNA polymerase required for transcription from promoters containing downstream basal promoter element GGGA. J Biol Chem (2008) 0.82
Phage-encoded inhibitor of Staphylococcus aureus transcription exerts context-dependent effects on promoter function in a modified Escherichia coli-based transcription system. J Bacteriol (2013) 0.82
Catching RNA polymerase in the act of binding: intermediates in transcription illuminated by synchrotron footprinting. Proc Natl Acad Sci U S A (2005) 0.81
Sequence-dependent upstream DNA-RNA polymerase interactions in the open complex with lambdaPR and lambdaPRM promoters and implications for the mechanism of promoter interference. J Mol Biol (2008) 0.80
Role of cis-acting sites in stimulation of the phage λ P(RM) promoter by CI-mediated looping. J Bacteriol (2013) 0.78
Fluorescence Resonance Energy Transfer Characterization of DNA Wrapping in Closed and Open Escherichia coli RNA Polymerase-λPR Promoter Complexes. Biochemistry (2016) 0.75
A procedure for the rapid, large-scall purification of Escherichia coli DNA-dependent RNA polymerase involving Polymin P precipitation and DNA-cellulose chromatography. Biochemistry (1975) 16.43
Mechanism and control of transcription initiation in prokaryotes. Annu Rev Biochem (1985) 11.99
Crystal structure of a CAP-DNA complex: the DNA is bent by 90 degrees. Science (1991) 11.45
A third recognition element in bacterial promoters: DNA binding by the alpha subunit of RNA polymerase. Science (1993) 7.42
Crystal structure of a bacterial RNA polymerase holoenzyme at 2.6 A resolution. Nature (2002) 6.74
Structural basis of transcription initiation: an RNA polymerase holoenzyme-DNA complex. Science (2002) 6.17
Crystal structure of an IHF-DNA complex: a protein-induced DNA U-turn. Cell (1996) 5.38
Biochemistry and structural biology of transcription factor IID (TFIID). Annu Rev Biochem (1996) 5.19
Structural basis of transcription initiation: RNA polymerase holoenzyme at 4 A resolution. Science (2002) 5.18
Quantitative model for gene regulation by lambda phage repressor. Proc Natl Acad Sci U S A (1982) 4.93
A simple procedure for resolution of Escherichia coli RNA polymerase holoenzyme from core polymerase. Arch Biochem Biophys (1977) 4.85
Structure of the bacterial RNA polymerase promoter specificity sigma subunit. Mol Cell (2002) 4.22
Structural basis of transcription: an RNA polymerase II-TFIIB cocrystal at 4.5 Angstroms. Science (2004) 3.46
Structural organization of bacterial RNA polymerase holoenzyme and the RNA polymerase-promoter open complex. Cell (2002) 3.21
Transcription activation at Class I CAP-dependent promoters. Mol Microbiol (1993) 2.90
Mechanism of activation of transcription initiation from the lambda PRM promoter. J Mol Biol (1982) 2.75
Factor independent activation of rrnB P1. An "extended" promoter with an upstream element that dramatically increases promoter strength. J Mol Biol (1994) 2.73
Kinetics of open complex formation between Escherichia coli RNA polymerase and the lac UV5 promoter. Evidence for a sequential mechanism involving three steps. Biochemistry (1985) 2.71
Structural basis of transcription activation: the CAP-alpha CTD-DNA complex. Science (2002) 2.67
UPs and downs in bacterial transcription initiation: the role of the alpha subunit of RNA polymerase in promoter recognition. Mol Microbiol (2000) 2.52
Mapping of single-stranded regions in duplex DNA at the sequence level: single-strand-specific cytosine methylation in RNA polymerase-promoter complexes. Proc Natl Acad Sci U S A (1983) 2.41
Structural organization of the RNA polymerase-promoter open complex. Cell (2000) 2.25
X-ray structure of the DNase I-d(GGTATACC)2 complex at 2.3 A resolution. J Mol Biol (1992) 2.19
Topography of intermediates in transcription initiation of E.coli. EMBO J (1990) 2.16
Bacterial promoter architecture: subsite structure of UP elements and interactions with the carboxy-terminal domain of the RNA polymerase alpha subunit. Genes Dev (1999) 2.13
Wrapping of DNA around the E.coli RNA polymerase open promoter complex. EMBO J (1999) 1.97
Escherichia coli promoters with UP elements of different strengths: modular structure of bacterial promoters. J Bacteriol (1998) 1.91
E. coli RNA polymerase, deleted in the C-terminal part of its alpha-subunit, interacts differently with the cAMP-CRP complex at the lacP1 and at the galP1 promoter. Nucleic Acids Res (1993) 1.88
Kinetics and mechanism of the interaction of Escherichia coli RNA polymerase with the lambda PR promoter. J Mol Biol (1984) 1.84
Variable structures of Fis-DNA complexes determined by flanking DNA-protein contacts. J Mol Biol (1996) 1.74
Three-dimensional structure of E. coli core RNA polymerase: promoter binding and elongation conformations of the enzyme. Cell (1995) 1.71
Structure of a ternary transcription activation complex. Mol Cell (2004) 1.68
HO. and DNase I probing of E sigma 70 RNA polymerase--lambda PR promoter open complexes: Mg2+ binding and its structural consequences at the transcription start site. Biochemistry (1995) 1.68
Tethering sigma70 to RNA polymerase reveals high in vivo activity of sigma factors and sigma70-dependent pausing at promoter-distal locations. Genes Dev (2003) 1.64
Mutations affecting two different steps in transcription initiation at the phage lambda PRM promoter. Proc Natl Acad Sci U S A (1983) 1.58
Both fis-dependent and factor-independent upstream activation of the rrnB P1 promoter are face of the helix dependent. Nucleic Acids Res (1992) 1.56
Sequence-independent upstream DNA-alphaCTD interactions strongly stimulate Escherichia coli RNA polymerase-lacUV5 promoter association. Proc Natl Acad Sci U S A (2004) 1.52
Two open complexes and a requirement for Mg2+ to open the lambda PR transcription start site. Science (1993) 1.51
Upstream A-tracts increase bacterial promoter activity through interactions with the RNA polymerase alpha subunit. Proc Natl Acad Sci U S A (1998) 1.42
A mutant RNA polymerase that forms unusual open promoter complexes. Proc Natl Acad Sci U S A (1997) 1.41
An intersubunit contact stimulating transcription initiation by E coli RNA polymerase: interaction of the alpha C-terminal domain and sigma region 4. Genes Dev (2003) 1.38
Changing the mechanism of transcriptional activation by phage lambda repressor. Proc Natl Acad Sci U S A (1997) 1.35
Regulation of the kinetics of the interaction of Escherichia coli RNA polymerase with the lambda PR promoter by salt concentration. Biochemistry (1985) 1.29
A genetic switch in a bacterial virus. Sci Am (1982) 1.28
Transcription activation by cAMP receptor protein (CRP) at the Escherichia coli gal P1 promoter. Crucial role for the spacing between the CRP binding site and the -10 region. Biochemistry (1992) 1.21
Upstream interactions at the lambda pRM promoter are sequence nonspecific and activate the promoter to a lesser extent than an introduced UP element of an rRNA promoter. J Bacteriol (1996) 1.14
On the role of the Escherichia coli RNA polymerase sigma 70 region 4.2 and alpha-subunit C-terminal domains in promoter complex formation on the extended -10 galP1 promoter. J Biol Chem (2003) 1.13
Mechanism for a transcriptional activator that works at the isomerization step. Proc Natl Acad Sci U S A (2000) 1.12
The 0 degree C closed complexes between Escherichia coli RNA polymerase and two promoters, T7-A3 and lacUV5. J Biol Chem (1987) 1.09
Promoter recognition by Escherichia coli RNA polymerase: effects of the UP element on open complex formation and promoter clearance. Biochemistry (1998) 1.06
Roles of Mg2+ in the mechanism of formation and dissociation of open complexes between Escherichia coli RNA polymerase and the lambda PR promoter: kinetic evidence for a second open complex requiring Mg2+. Biochemistry (1992) 1.02
Interference by PR-bound RNA polymerase with PRM function in vitro. Modulation by the bacteriophage lambda cI protein. J Biol Chem (1993) 1.00
Promoter resurrection by activators--a minireview. Gene (1993) 0.96
Novel computer program for fast exact calculation of accessible and molecular surface areas and average surface curvature. J Comput Chem (2002) 3.00
Mechanism of bacterial transcription initiation: RNA polymerase - promoter binding, isomerization to initiation-competent open complexes, and initiation of RNA synthesis. J Mol Biol (2011) 2.50
Synthesis-mediated release of a small RNA inhibitor of RNA polymerase. Science (2006) 1.95
Crowding and confinement effects on protein diffusion in vivo. J Bacteriol (2006) 1.84
Hofmeister salt effects on surface tension arise from partitioning of anions and cations between bulk water and the air-water interface. J Phys Chem B (2007) 1.77
The exclusion of glycine betaine from anionic biopolymer surface: why glycine betaine is an effective osmoprotectant but also a compatible solute. Biochemistry (2004) 1.52
Thermodynamic origin of hofmeister ion effects. J Phys Chem B (2008) 1.50
Roles of cytoplasmic osmolytes, water, and crowding in the response of Escherichia coli to osmotic stress: biophysical basis of osmoprotection by glycine betaine. Biochemistry (2003) 1.48
Real-time footprinting of DNA in the first kinetically significant intermediate in open complex formation by Escherichia coli RNA polymerase. Proc Natl Acad Sci U S A (2007) 1.44
Protein surface salt bridges and paths for DNA wrapping. Curr Opin Struct Biol (2002) 1.37
Cytoplasmic protein mobility in osmotically stressed Escherichia coli. J Bacteriol (2008) 1.34
Preferential interactions of glycine betaine and of urea with DNA: implications for DNA hydration and for effects of these solutes on DNA stability. Biochemistry (2004) 1.31
Use of urea and glycine betaine to quantify coupled folding and probe the burial of DNA phosphates in lac repressor-lac operator binding. Biochemistry (2005) 1.31
Protein diffusion in the periplasm of E. coli under osmotic stress. Biophys J (2011) 1.30
Why Hofmeister effects of many salts favor protein folding but not DNA helix formation. Proc Natl Acad Sci U S A (2010) 1.30
Interactions of the osmolyte glycine betaine with molecular surfaces in water: thermodynamics, structural interpretation, and prediction of m-values. Biochemistry (2009) 1.29
Quantifying why urea is a protein denaturant, whereas glycine betaine is a protein stabilizer. Proc Natl Acad Sci U S A (2011) 1.27
Separation of preferential interaction and excluded volume effects on DNA duplex and hairpin stability. Proc Natl Acad Sci U S A (2011) 1.26
Partitioning of atmospherically relevant ions between bulk water and the water/vapor interface. Proc Natl Acad Sci U S A (2006) 1.23
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 (2007) 1.18
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 (2008) 1.17
Urea-amide preferential interactions in water: quantitative comparison of model compound data with biopolymer results using water accessible surface areas. J Phys Chem B (2007) 1.16
Large changes in cytoplasmic biopolymer concentration with osmolality indicate that macromolecular crowding may regulate protein-DNA interactions and growth rate in osmotically stressed Escherichia coli K-12. J Mol Recognit (2004) 1.16
Thermal and urea-induced unfolding of the marginally stable lac repressor DNA-binding domain: a model system for analysis of solute effects on protein processes. Biochemistry (2003) 1.15
Application of the local-bulk partitioning and competitive binding models to interpret preferential interactions of glycine betaine and urea with protein surface. Biochemistry (2004) 1.11
Effect of the number of nucleic acid oligomer charges on the salt dependence of stability (DeltaG 37degrees) and melting temperature (Tm): NLPB analysis of experimental data. Biochemistry (2004) 1.10
Generalized derivation of an exact relationship linking different coefficients that characterize thermodynamic effects of preferential interactions. Biophys Chem (2002) 1.08
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 (2010) 1.07
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 (2010) 1.05
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 (2007) 1.04
Methods of changing biopolymer volume fraction and cytoplasmic solute concentrations for in vivo biophysical studies. Methods Enzymol (2007) 1.00
Probing the protein-folding mechanism using denaturant and temperature effects on rate constants. Proc Natl Acad Sci U S A (2013) 0.98
Interactions of the KWK6 cationic peptide with short nucleic acid oligomers: demonstration of large Coulombic end effects on binding at 0.1-0.2 M salt. Nucleic Acids Res (2004) 0.96
DNA binding mode transitions of Escherichia coli HU(alphabeta): evidence for formation of a bent DNA--protein complex on intact, linear duplex DNA. J Mol Biol (2008) 0.95
Thermodynamics and folding pathway of tetraloop receptor-mediated RNA helical packing. J Mol Biol (2008) 0.91
Key roles of the downstream mobile jaw of Escherichia coli RNA polymerase in transcription initiation. Biochemistry (2012) 0.90
Preferential interactions in aqueous solutions of urea and KCl. Biophys Chem (2003) 0.90
Quantifying functional group interactions that determine urea effects on nucleic acid helix formation. J Am Chem Soc (2013) 0.89
Gibbs-Duhem-based relationships among derivatives expressing the concentration dependences of selected chemical potentials for a multicomponent system. Biophys Chem (2004) 0.89
Quantifying additive interactions of the osmolyte proline with individual functional groups of proteins: comparisons with urea and glycine betaine, interpretation of m-values. Biochemistry (2013) 0.87
Interactions of cationic ligands and proteins with small nucleic acids: analytic treatment of the large coulombic end effect on binding free energy as a function of salt concentration. Biochemistry (2006) 0.86
Using surface tension data to predict differences in surface and bulk concentrations of nonelectrolytes in water. J Phys Chem C Nanomater Interfaces (2009) 0.84
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 (2009) 0.83
Nonspecific DNA binding and bending by HUαβ: interfaces of the three binding modes characterized by salt-dependent thermodynamics. J Mol Biol (2011) 0.83
Asymptotic solution of the cylindrical nonlinear Poisson-Boltzmann equation at low salt concentration: analytic expressions for surface potential and preferential interaction coefficient. Proc Natl Acad Sci U S A (2002) 0.82
Positioning the Intracellular Salt Potassium Glutamate in the Hofmeister Series by Chemical Unfolding Studies of NTL9. Biochemistry (2016) 0.80
Using solutes and kinetics to probe large conformational changes in the steps of transcription initiation. Methods Mol Biol (2015) 0.78
Correction to "quantifying functional group interactions that determine urea effects on nucleic Acid helix formation". J Am Chem Soc (2013) 0.78
Rapid quench mixing to quantify kinetics of steps in association of Escherichia coli RNA polymerase with promoter DNA. Methods Enzymol (2003) 0.77
Contributions of the histidine side chain and the N-terminal alpha-amino group to the binding thermodynamics of oligopeptides to nucleic acids as a function of pH. Biochemistry (2010) 0.76