Published in Biochim Biophys Acta on November 30, 2012
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Rapid kinetic analysis of transcription elongation by Escherichia coli RNA polymerase. J Mol Biol (2008) 1.03
Millisecond phase kinetic analysis of elongation catalyzed by human, yeast, and Escherichia coli RNA polymerase. Methods (2009) 1.03
Molecular dynamics and mutational analysis of the catalytic and translocation cycle of RNA polymerase. BMC Biophys (2012) 0.99
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RNA polymerase II flexibility during translocation from normal mode analysis. Proteins (2010) 0.97
Templated nucleoside triphosphate binding to a noncatalytic site on RNA polymerase regulates transcription. Proc Natl Acad Sci U S A (2011) 0.91
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The Bridge Helix of RNA polymerase acts as a central nanomechanical switchboard for coordinating catalysis and substrate movement. Archaea (2012) 0.84
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Rapid pyrophosphate release from transcriptional elongation complexes appears to be coupled to a nucleotide-induced conformational change in E. coli core polymerase. J Mol Biol (2011) 0.82
Cation-π interactions induce kinking of a molecular hinge in the RNA polymerase bridge-helix domain. Biochem Soc Trans (2011) 0.81
CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing. Nature (2011) 5.50
Structural basis for transcription elongation by bacterial RNA polymerase. Nature (2007) 5.09
Sensing small molecules by nascent RNA: a mechanism to control transcription in bacteria. Cell (2002) 4.67
A ratchet mechanism of transcription elongation and its control. Cell (2005) 4.48
Structural basis for substrate loading in bacterial RNA polymerase. Nature (2007) 4.40
Nucleosome remodeling induced by RNA polymerase II: loss of the H2A/H2B dimer during transcription. Mol Cell (2002) 3.91
Cooperation between translating ribosomes and RNA polymerase in transcription elongation. Science (2010) 3.87
Nucleosomal fluctuations govern the transcription dynamics of RNA polymerase II. Science (2009) 3.60
Regulation through the secondary channel--structural framework for ppGpp-DksA synergism during transcription. Cell (2004) 3.39
A decade of riboswitches. Cell (2013) 3.26
The riboswitch-mediated control of sulfur metabolism in bacteria. Proc Natl Acad Sci U S A (2003) 2.83
RNA-mediated response to heat shock in mammalian cells. Nature (2006) 2.79
H2S: a universal defense against antibiotics in bacteria. Science (2011) 2.69
Transcription termination control of the S box system: direct measurement of S-adenosylmethionine by the leader RNA. Proc Natl Acad Sci U S A (2003) 2.68
Termination factor Rho and its cofactors NusA and NusG silence foreign DNA in E. coli. Science (2008) 2.66
Backtracking determines the force sensitivity of RNAP II in a factor-dependent manner. Nature (2007) 2.64
Structural basis for converting a general transcription factor into an operon-specific virulence regulator. Mol Cell (2007) 2.56
Nature of the nucleosomal barrier to RNA polymerase II. Mol Cell (2005) 2.55
Cooperation between RNA polymerase molecules in transcription elongation. Science (2003) 2.47
Endogenous nitric oxide protects bacteria against a wide spectrum of antibiotics. Science (2009) 2.32
Extensive functional overlap between sigma factors in Escherichia coli. Nat Struct Mol Biol (2006) 2.30
Transient reversal of RNA polymerase II active site closing controls fidelity of transcription elongation. Mol Cell (2008) 2.21
Linking RNA polymerase backtracking to genome instability in E. coli. Cell (2011) 2.20
Riboswitch control of Rho-dependent transcription termination. Proc Natl Acad Sci U S A (2012) 2.10
Mechanism of translesion transcription by RNA polymerase II and its role in cellular resistance to DNA damage. Mol Cell (2012) 1.96
Mechanism of sequence-specific pausing of bacterial RNA polymerase. Proc Natl Acad Sci U S A (2009) 1.92
Transcription through the roadblocks: the role of RNA polymerase cooperation. EMBO J (2003) 1.89
Mechanism of chromatin remodeling and recovery during passage of RNA polymerase II. Nat Struct Mol Biol (2009) 1.86
Shortening of RNA:DNA hybrid in the elongation complex of RNA polymerase is a prerequisite for transcription termination. Mol Cell (2002) 1.83
NO-mediated cytoprotection: instant adaptation to oxidative stress in bacteria. Proc Natl Acad Sci U S A (2005) 1.81
The downstream DNA jaw of bacterial RNA polymerase facilitates both transcriptional initiation and pausing. J Biol Chem (2002) 1.79
An allosteric mechanism of Rho-dependent transcription termination. Nature (2010) 1.73
An allosteric path to transcription termination. Mol Cell (2007) 1.73
Mutations of bacterial RNA polymerase leading to resistance to microcin j25. J Biol Chem (2002) 1.67
Structural basis for transcription inhibition by tagetitoxin. Nat Struct Mol Biol (2005) 1.64
Transcription inactivation through local refolding of the RNA polymerase structure. Nature (2008) 1.63
Thermodynamic and kinetic modeling of transcriptional pausing. Proc Natl Acad Sci U S A (2006) 1.61
Termination and antitermination: RNA polymerase runs a stop sign. Nat Rev Microbiol (2011) 1.59
Transcription-replication encounters, consequences and genomic instability. Nat Struct Mol Biol (2013) 1.54
The β subunit gate loop is required for RNA polymerase modification by RfaH and NusG. Mol Cell (2011) 1.49
Bacillus anthracis-derived nitric oxide is essential for pathogen virulence and survival in macrophages. Proc Natl Acad Sci U S A (2008) 1.49
RNA polymerase holoenzyme: structure, function and biological implications. Curr Opin Microbiol (2003) 1.48
Mutations in the Saccharomyces cerevisiae RPB1 gene conferring hypersensitivity to 6-azauracil. Genetics (2006) 1.47
Riboswitch-dependent gene regulation and its evolution in the plant kingdom. Genes Dev (2007) 1.47
Nucleosomal elements that control the topography of the barrier to transcription. Cell (2012) 1.46
Functional specialization of transcription elongation factors. EMBO J (2008) 1.46
RNA polymerase: the vehicle of transcription. Trends Microbiol (2008) 1.45
Dynamic error correction and regulation of downstream bubble opening by human RNA polymerase II. Mol Cell (2005) 1.43
Synergistic action of RNA polymerases in overcoming the nucleosomal barrier. Nat Struct Mol Biol (2010) 1.43
Allosteric control of the RNA polymerase by the elongation factor RfaH. Nucleic Acids Res (2007) 1.43
Bacterial nitric-oxide synthases operate without a dedicated redox partner. J Biol Chem (2008) 1.41
Targeting eEF1A by a Legionella pneumophila effector leads to inhibition of protein synthesis and induction of host stress response. Cell Microbiol (2009) 1.36
Bacterial polymerase and yeast polymerase II use similar mechanisms for transcription through nucleosomes. J Biol Chem (2003) 1.36
An α helix to β barrel domain switch transforms the transcription factor RfaH into a translation factor. Cell (2012) 1.35
Bacterial nitric oxide extends the lifespan of C. elegans. Cell (2013) 1.35
Engineering of elongation complexes of bacterial and yeast RNA polymerases. Methods Enzymol (2003) 1.31
Chromatin remodeling by RNA polymerases. Trends Biochem Sci (2004) 1.30
Regulation through the RNA polymerase secondary channel. Structural and functional variability of the coiled-coil transcription factors. J Biol Chem (2005) 1.29
The elongation factor RfaH and the initiation factor sigma bind to the same site on the transcription elongation complex. Proc Natl Acad Sci U S A (2008) 1.29
Discrimination against deoxyribonucleotide substrates by bacterial RNA polymerase. J Biol Chem (2004) 1.29
Rpb9 subunit controls transcription fidelity by delaying NTP sequestration in RNA polymerase II. J Biol Chem (2009) 1.25
NTP-driven translocation by human RNA polymerase II. J Biol Chem (2003) 1.24
Catalysis of S-nitrosothiols formation by serum albumin: the mechanism and implication in vascular control. Proc Natl Acad Sci U S A (2002) 1.23
Allosteric control of catalysis by the F loop of RNA polymerase. Proc Natl Acad Sci U S A (2009) 1.20
Alpha-amanitin blocks translocation by human RNA polymerase II. J Biol Chem (2004) 1.20
Assessment of nitric oxide signals by triiodide chemiluminescence. Proc Natl Acad Sci U S A (2007) 1.20
Assays and affinity purification of biotinylated and nonbiotinylated forms of double-tagged core RNA polymerase II from Saccharomyces cerevisiae. Methods Enzymol (2003) 1.19
The elongation rate of RNA polymerase determines the fate of transcribed nucleosomes. Nat Struct Mol Biol (2011) 1.19
Transcription factors IIF and IIS and nucleoside triphosphate substrates as dynamic probes of the human RNA polymerase II mechanism. J Mol Biol (2004) 1.17
Therapeutic effect of exogenous hsp70 in mouse models of Alzheimer's disease. J Alzheimers Dis (2014) 1.16
Functional regions of the N-terminal domain of the antiterminator RfaH. Mol Microbiol (2010) 1.15
RNA polymerase II with open and closed trigger loops: active site dynamics and nucleic acid translocation. Biophys J (2010) 1.14
Molecular dynamics of apo-adenylate kinase: a distance replica exchange method for the free energy of conformational fluctuations. J Phys Chem B (2006) 1.14
Tagetitoxin inhibits RNA polymerase through trapping of the trigger loop. J Biol Chem (2011) 1.14
Complete dissection of transcription elongation reveals slow translocation of RNA polymerase II in a linear ratchet mechanism. Elife (2013) 1.14
Multiscale multiphysics and multidomain models--flexibility and rigidity. J Chem Phys (2013) 1.13
Translocation by multi-subunit RNA polymerases. Biochim Biophys Acta (2010) 1.13
The carboxy-terminal coiled-coil of the RNA polymerase beta'-subunit is the main binding site for Gre factors. EMBO Rep (2007) 1.13
Combinatorial control of human RNA polymerase II (RNAP II) pausing and transcript cleavage by transcription factor IIF, hepatitis delta antigen, and stimulatory factor II. J Biol Chem (2003) 1.12
Transcription regulatory elements are punctuation marks for DNA replication. Proc Natl Acad Sci U S A (2006) 1.12
Water chain formation and possible proton pumping routes in Rhodobacter sphaeroides cytochrome c oxidase: a molecular dynamics comparison of the wild type and R481K mutant. Biochemistry (2005) 1.12
Methicillin-resistant Staphylococcus aureus bacterial nitric-oxide synthase affects antibiotic sensitivity and skin abscess development. J Biol Chem (2013) 1.11
Sensitivity of mitochondrial transcription and resistance of RNA polymerase II dependent nuclear transcription to antiviral ribonucleosides. PLoS Pathog (2012) 1.11
Isolation and characterization of RNA polymerase rpoB mutations that alter transcription slippage during elongation in Escherichia coli. J Biol Chem (2012) 1.10
Functional analysis of Thermus thermophilus transcription factor NusG. Nucleic Acids Res (2010) 1.08
Transcriptional pausing coordinates folding of the aptamer domain and the expression platform of a riboswitch. Proc Natl Acad Sci U S A (2012) 1.07
Macromolecular micromovements: how RNA polymerase translocates. Curr Opin Struct Biol (2009) 1.07
Conformational coupling, bridge helix dynamics and active site dehydration in catalysis by RNA polymerase. Biochim Biophys Acta (2010) 1.06