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Mechanism of Bacterial Transcription Initiation: RNA Polymerase - Promoter Binding, Isomerization to Initiation-Competent Open Complexes, and Initiation of RNA Synthesis

Journal of molecular biology, 2011-10, Vol.412 (5), p.754-771

2011

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Stepwise Promoter Melting by Bacterial RNA Polymerase

Molecular cell, 2020-04, Vol.78 (2), p.275-288.e6

2020

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Structure and function of the mycobacterial transcription initiation complex with the essential regulator RbpA

eLife, 2017-01, Vol.6 (2017)

2017

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Time-resolved cryo-EM using Spotiton

Nature methods, 2020-09, Vol.17 (9), p.897-900

2020

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Structural origins of Escherichia coli RNA polymerase open promoter complex stability

Proceedings of the National Academy of Sciences - PNAS, 2021-10, Vol.118 (40), p.1

2021

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Synthesis-Mediated Release of a Small RNA Inhibitor of RNA Polymerase

Science (American Association for the Advancement of Science), 2006-12, Vol.314 (5805), p.1601-1603

2006

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Early intermediates in bacterial RNA polymerase promoter melting visualized by time-resolved cryo-electron microscopy

Nature structural & molecular biology, 2024-07

2024

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Native Mass Spectrometry-Based Screening for Optimal Sample Preparation in Single-Particle Cryo-EM

Structure (London), 2021-02, Vol.29 (2), p.186-195.e6

2021

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Transcription initiation in mycobacteria: a biophysical perspective

Transcription, 2020-03, Vol.11 (2), p.53-65

2020

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Interactions of the Osmolyte Glycine Betaine with Molecular Surfaces in Water: Thermodynamics, Structural Interpretation, and Prediction of m-Values

Biochemistry (Easton), 2009-11, Vol.48 (43), p.10372-10379

2009

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One-step DNA melting in the RNA polymerase cleft opens the initiation bubble to form an unstable open complex

Proceedings of the National Academy of Sciences - PNAS, 2010-06, Vol.107 (23), p.10418-10423

2010

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Probing DNA Binding, DNA Opening, and Assembly of a Downstream Clamp/Jaw in Escherichia coli RNA Polymerase−λPR Promoter Complexes Using Salt and the Physiological Anion Glutamate

Biochemistry (Easton), 2010-05, Vol.49 (20), p.4361-4373

2010

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Real-time footprinting of DNA in the first kinetically significant intermediate in open complex formation by Escherichia coli RNA polymerase

Proceedings of the National Academy of Sciences - PNAS, 2007-05, Vol.104 (19), p.7833-7838

2007

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Nonspecific DNA Binding and Bending by HU αβ: Interfaces of the Three Binding Modes Characterized by Salt-Dependent Thermodynamics

Journal of molecular biology, 2011-07, Vol.410 (2), p.241-267

2011

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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

Journal of molecular biology, 2008-03, Vol.377 (1), p.9-27

2008

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Enthalpy and Heat Capacity Changes for Formation of an Oligomeric DNA Duplex: Interpretation in Terms of Coupled Processes of Formation and Association of Single-Stranded Helices

Biochemistry (Easton), 1999-06, Vol.38 (26), p.8409-8422

1999

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Preferential Interactions of Glycine Betaine and of Urea with DNA: Implications for DNA Hydration and for Effects of These Solutes on DNA Stability

Biochemistry (Easton), 2004-11, Vol.43 (46), p.14744-14758

2004

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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

Journal of molecular biology, 2009-01, Vol.385 (2), p.339-349

2009

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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

Journal of molecular biology, 2008-02, Vol.376 (4), p.1034-1047

2008

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DNA Binding Mode Transitions of Escherichia coli HU αβ: Evidence for Formation of a Bent DNA — Protein Complex on Intact, Linear Duplex DNA

Journal of molecular biology, 2008-11, Vol.383 (2), p.324-346

2008

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Use of Urea and Glycine Betaine To Quantify Coupled Folding and Probe the Burial of DNA Phosphates in Lac Repressor−Lac Operator Binding

Biochemistry (Easton), 2005-12, Vol.44 (51), p.16896-16911

2005

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The Effects of Upstream DNA on Open Complex Formation by Escherichia coli RNA Polymerase

Proceedings of the National Academy of Sciences - PNAS, 2005-01, Vol.102 (2), p.285-290

2005

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Protein surface salt bridges and paths for DNA wrapping

Current Opinion in Structural Biology, 2002-06, Vol.12 (3), p.311-319

2002

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Solute Probes of Conformational Changes in Open Complex (RPo) Formation by Escherichia coli RNA Polymerase at the λPR Promoter: Evidence for Unmasking of the Active Site in the Isomerization Step and for Large-Scale Coupled Folding in the Subsequent Conversion to RPo

Biochemistry (Easton), 2006-02, Vol.45 (7), p.2161-2177

2006

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Do Sigma Factors Need Help with a Meltdown?

Cell, 2006-10, Vol.127 (2), p.256-258

2006

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Mechanism of Bacterial Transcription Initiation: RNA Polymerase - Promoter Binding, Isomerization to Initiation-Competent Open Complexes, and Initiation of RNA Synthesis

Stepwise Promoter Melting by Bacterial RNA Polymerase

Structure and function of the mycobacterial transcription initiation complex with the essential regulator RbpA

Time-resolved cryo-EM using Spotiton

Structural origins of Escherichia coli RNA polymerase open promoter complex stability

Synthesis-Mediated Release of a Small RNA Inhibitor of RNA Polymerase

Early intermediates in bacterial RNA polymerase promoter melting visualized by time-resolved cryo-electron microscopy

Native Mass Spectrometry-Based Screening for Optimal Sample Preparation in Single-Particle Cryo-EM

Transcription initiation in mycobacteria: a biophysical perspective

Interactions of the Osmolyte Glycine Betaine with Molecular Surfaces in Water: Thermodynamics, Structural Interpretation, and Prediction of m-Values

One-step DNA melting in the RNA polymerase cleft opens the initiation bubble to form an unstable open complex

Probing DNA Binding, DNA Opening, and Assembly of a Downstream Clamp/Jaw in Escherichia coli RNA Polymerase−λPR Promoter Complexes Using Salt and the Physiological Anion Glutamate

Real-time footprinting of DNA in the first kinetically significant intermediate in open complex formation by Escherichia coli RNA polymerase

Nonspecific DNA Binding and Bending by HU αβ: Interfaces of the Three Binding Modes Characterized by Salt-Dependent Thermodynamics

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

Enthalpy and Heat Capacity Changes for Formation of an Oligomeric DNA Duplex: Interpretation in Terms of Coupled Processes of Formation and Association of Single-Stranded Helices

Preferential Interactions of Glycine Betaine and of Urea with DNA: Implications for DNA Hydration and for Effects of These Solutes on DNA Stability

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

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

DNA Binding Mode Transitions of Escherichia coli HU αβ: Evidence for Formation of a Bent DNA — Protein Complex on Intact, Linear Duplex DNA

Use of Urea and Glycine Betaine To Quantify Coupled Folding and Probe the Burial of DNA Phosphates in Lac Repressor−Lac Operator Binding

The Effects of Upstream DNA on Open Complex Formation by Escherichia coli RNA Polymerase

Protein surface salt bridges and paths for DNA wrapping

Solute Probes of Conformational Changes in Open Complex (RPo) Formation by Escherichia coli RNA Polymerase at the λPR Promoter: Evidence for Unmasking of the Active Site in the Isomerization Step and for Large-Scale Coupled Folding in the Subsequent Conversion to RPo

Do Sigma Factors Need Help with a Meltdown?

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