R. Ebright

发表

Indirect readout of DNA sequence at the primary-kink site in the CAP-DNA complex: alteration of DNA binding specificity through alteration of DNA kinking.

T. Kunkel, S. Chen, A. Gunasekera, 2001, Journal of molecular biology.

Bacterial promoter architecture: subsite structure of UP elements and interactions with the carboxy-terminal domain of the RNA polymerase alpha subunit.

R. Ebright, R. Gourse, Z. Chen, 1999, Genes & development.

Dynamically driven protein allostery

R. Ebright, C. Kalodimos, N. Popovych, 2006, Nature Structural &Molecular Biology.

Sensory Biology Plant Genetics Protein Biochemistry Developmental Biology Computational Bioinformatics Laboratory Plastid Molecular Genetics Molecular Genetics of Meiotic Recombination & Chromosome Segregation Molecular Biology of Plant Development Plant Genomics & Bioinformatics Regulation of Gene

R. Ebright, A. Chakraborty, M. Barr, 2022 .

Promoter unwinding and promoter clearance by RNA polymerase: detection by single-molecule DNA nanomanipulation.

R. Ebright, A. Revyakin, T. Strick, 2004, Proceedings of the National Academy of Sciences of the United States of America.

Transcription activation at Class I CAP‐dependent promoters

R. Ebright, 1993, Molecular microbiology.

Transcription activation by catabolite activator protein (CAP).

R. Ebright, S. Busby, Steve Busby, 1999, Journal of molecular biology.

Retention of transcription initiation factor sigma70 in transcription elongation: single-molecule analysis.

T. Laurence, R. Ebright, S. Weiss, 2005, Molecular cell.

Bacterial RNA polymerase subunit omega and eukaryotic RNA polymerase subunit RPB6 are sequence, structural, and functional homologs and promote RNA polymerase assembly.

R. Ebright, K. Severinov, S. Darst, 2001, Proceedings of the National Academy of Sciences of the United States of America.

Accurate FRET measurements within single diffusing biomolecules using alternating-laser excitation.

Nam Ki Lee, R. Ebright, S. Weiss, 2005, Biophysical journal.

Structural basis of transcription inhibition by fidaxomicin (lipiarmycin A3)

R. Ebright, A. Kapanidis, E. Eng, 2017, bioRxiv.

Direct observation of abortive initiation and promoter escape within single immobilized transcription complexes.

R. Ebright, S. Weiss, A. Kapanidis, 2006, Biophysical journal.

Structural Basis of Transcription Initiation

R. Ebright, S. Tuske, E. Arnold, 2012, Science.

Random mutagenesis of gene-sized DNA molecules by use of PCR with Taq DNA polymerase.

X P Zhang, X. Zhang, R. Ebright, 1991, Nucleic acids research.

Structural Organization of the RNA Polymerase-Promoter Open Complex

Younggyu Kim, R. Ebright, A. Revyakin, 2000, Cell.

DNA-sequence recognition by CAP: role of the adenine N6 atom of base pair 6 of the DNA site.

A. Gunasekera, R. Ebright, Y. Ebright, 1990, Nucleic acids research.

Substitution of 2 base pairs (1 base pair per DNA half-site) within the Escherichia coli lac promoter DNA site for catabolite gene activator protein places the lac promoter in the FNR regulon.

X. Zhang, R. Ebright, 1990, The Journal of biological chemistry.

Aromatic hydrogen bond in sequence-specific protein DNA recognition

Gary Parkinson, Helen Berman, Thomas A. Kunkel, 1996, Nature Structural Biology.

Indirect readout of DNA sequence at the primary-kink site in the CAP-DNA complex: DNA binding specificity based on energetics of DNA kinking.

H M Berman, S. Chen, R. Ebright, 2001, Journal of molecular biology.

Soma Mandal Graduate Assistant

R. Ebright, H. Berman, J. Flippen-Anderson, 2022 .

Antibacterial peptide microcin J25 inhibits transcription by binding within and obstructing the RNA polymerase secondary channel.

Jennifer L. Knight, Ronald M Levy, Jayanta Mukhopadhyay, 2004, Molecular cell.

Abortive Initiation and Productive Initiation by RNA Polymerase Involve DNA Scrunching

Terence R. Strick, Richard H. Ebright, R. Ebright, 2006, Science.

Site-specific incorporation of fluorescent probes into protein: hexahistidine-tag-mediated fluorescent labeling with (Ni(2+):nitrilotriacetic Acid (n)-fluorochrome conjugates.

R. Ebright, A. Kapanidis, Y. Ebright, 2001, Journal of the American Chemical Society.

RNA polymerase clamp conformational dynamics: long-lived states and modulation by crowding, cations, and nonspecific DNA binding

R. Ebright, A. Kapanidis, Abhishek Mazumder, 2020, bioRxiv.

Mutations that alter the DNA sequence specificity of the catabolite gene activator protein of E. coli

Pascale Cossart, Richard H. Ebright, Jon Beckwith, 1984, Nature.

Initial Transcription by RNA Polymerase Proceeds Through a DNA-Scrunching Mechanism

Shimon Weiss, Achillefs N. Kapanidis, Emmanuel Margeat, 2006, Science.

Thermodynamic and kinetic modeling of transcriptional pausing.

Anirvan M. Sengupta, Anirvan M Sengupta, Vitaly Epshtein, 2006, Proceedings of the National Academy of Sciences of the United States of America.

Staphylococcus aureus Costs of Resistance to Myxopyronin in Frequency, Spectrum, and Nonzero Fitness

R. Ebright, Y. Ebright, David Degen, 2012 .

Frequency, Spectrum, and Nonzero Fitness Costs of Resistance to Myxopyronin in Staphylococcus aureus

R. Ebright, Y. Ebright, David Degen, 2012, Antimicrobial Agents and Chemotherapy.

Analogs of cyclic AMP that elicit the biochemically defined conformational change in catabolite gene activator protein (CAP) but do not stimulate binding to DNA.

R. Ebright, S. L. Le Grice, J. Krakow, 1985, Journal of molecular biology.

The functional subunit of a dimeric transcription activator protein depends on promoter architecture

R. Ebright, S. Busby, P. S. Pendergrast, 1994 .

RNA polymerase-DNA interaction: structures of intermediate, open, and elongation complexes.

R. Ebright, 1998, Cold Spring Harbor symposia on quantitative biology.

Binding of 2-hydroxybenzo(a)pyrene to estrogen receptors in rat cytosol.

R. Ebright, L. B. Chen, J. R. Wong, 1986, Cancer research.

The Initiation Factor TFE and the Elongation Factor Spt4/5 Compete for the RNAP Clamp during Transcription Initiation and Elongation

J. Michaelis, R. Ebright, A. Chakraborty, 2011, Molecular cell.

Design, Synthesis, and Characterization of TNP-2198, a Dual-Targeted Rifamycin-Nitroimidazole Conjugate with Potent Activity against Microaerophilic and Anaerobic Bacterial Pathogens

R. Ebright, Jing Chen, G. Robertson, 2022, Journal of medicinal chemistry.

Promoter-sequence determinants and structural basis of primer-dependent transcription initiation in Escherichia coli

Deanne M. Taylor, J. Kinney, R. Ebright, 2021, Proceedings of the National Academy of Sciences.

Structural basis of ECF-σ-factor-dependent transcription initiation

R. Ebright, K. Das, Sukhendu Mandal, 2018, Nature Communications.

Transcription inhibition by the depsipeptide antibiotic salinamide A

R. Ebright, E. Arnold, N. Connell, 2014, eLife.

RNA POLYMERASE INHIBITOR ACTIVITY AGAINST STAPHYLOCOCCUS EPIDERMIDIS BIOFILMS

R. Ebright, M. Chikindas, 2014 .

An appeal for an objective, open, and transparent scientific debate about the origin of SARS-CoV-2

J. Claverie, J. van Helden, R. Ebright, 2021, The Lancet.

Identification of amino acid‐base contacts in the Myc‐DNA complex by site‐specific bromouracil mediated photocrosslinking.

R. Ebright, Y. Ebright, Q. Dong, 1994, The EMBO journal.

Discovery, properties, and biosynthesis of pseudouridimycin, an antibacterial nucleoside-analog inhibitor of bacterial RNA polymerase

R. Ebright, S. Donadio, M. Sosio, 2019, Journal of Industrial Microbiology & Biotechnology.

Structural basis of Q-dependent antitermination

R. Ebright, Z. Yin, J. Kaelber, 2019, Proceedings of the National Academy of Sciences.

Structural basis of ECF-sigma-factor-dependent transcription initiation.

R. Ebright, K. Das, Sukhendu Mandal, 2019 .

Mitochondrial RNA capping: highly efficient 5’-RNA capping with NAD+ and NADH by yeast and human mitochondrial RNA polymerase

R. Ebright, D. Temiakov, Smita S. Patel, 2018, bioRxiv.

Highly efficient 5' capping of mitochondrial RNA with NAD+ and NADH by yeast and human mitochondrial RNA polymerase

R. Ebright, D. Wallace, D. Temiakov, 2018, eLife.

“CapZyme-Seq” comprehensively defines promoter-sequence determinants for RNA 5’ capping with NAD+

Deanne M. Taylor, R. Ebright, I. Barvík, 2017, bioRxiv.

Structural and mechanistic basis of σ-dependent transcriptional pausing.

J. Kinney, R. Ebright, Z. Yin, 2022, Proceedings of the National Academy of Sciences of the United States of America.

The interaction between sigma70 and the beta-flap of Escherichia coli RNA polymerase inhibits extension of nascent RNA during early elongation.

R. Ebright, K. Severinov, A. Hochschild, 2005, Proceedings of the National Academy of Sciences of the United States of America.

The RNA polymerase clamp interconverts dynamically among three states and is stabilized in a partly closed state by ppGpp

R. Ebright, A. Kapanidis, Abhishek Mazumder, 2018, bioRxiv.

The antibacterial threaded-lasso peptide capistruin inhibits bacterial RNA polymerase.

R. Ebright, M. Marahiel, K. Severinov, 2011, Journal of molecular biology.

Systematic Structure-Activity Analysis of Microcin J25*

R. Ebright, K. Severinov, J. Mukhopadhyay, 2008, Journal of Biological Chemistry.

Structure of antibacterial peptide microcin J25: a 21-residue lariat protoknot.

G. Montelione, R. Ebright, P. Dawson, 2003, Journal of the American Chemical Society.

N-(iodoacetyl)-p-phenylenediamine-EDTA: a reagent for high-efficiency incorporation of an EDTA-metal complex at a rationally selected site within a protein.

R. Ebright, Y. Ebright, R. Ludescher, 1993, Bioconjugate chemistry.

An Open Letter to Elias Zerhouni

Jeffrey W. Roberts, N. Cozzarelli, C. Yanofsky, 2005, Science.

Metabolomic investigation of the pseudouridimycin producer, a prolific streptomycete

R. Ebright, S. Donadio, M. Sosio, 2020, bioRxiv.

Analysis of the Pseudouridimycin Biosynthetic Pathway Provides Insights into the Formation of C-nucleoside Antibiotics.

R. Ebright, M. Medema, S. Donadio, 2018, Cell chemical biology.

Domain organization of RNA polymerase α subunit: C-terminal 85 amino acids constitute a domain capable of dimerization and DNA binding

R. Ebright, R. Gourse, W. Ross, 1994, Cell.

Salinamide F, new depsipeptide antibiotic and inhibitor of bacterial RNA polymerase from a marine-derived Streptomyces sp.

R. Ebright, David Degen, H. Hassan, 2014, The Journal of Antibiotics.

Closing and opening of the RNA polymerase trigger loop

R. Ebright, A. Kapanidis, Abhishek Mazumder, 2019, Proceedings of the National Academy of Sciences.

In transcription antitermination by Qλ, NusA induces refolding of Qλ to form a nozzle that extends the RNA polymerase RNA-exit channel

R. Ebright, Z. Yin, J. Kaelber, 2022, Proceedings of the National Academy of Sciences of the United States of America.

Static and kinetic site-specific protein-DNA photocrosslinking: analysis of bacterial transcription initiation complexes.

R. Ebright, V. Mekler, S. Druzhinin, 2009, Methods in molecular biology.

Site-specific protein-DNA photocrosslinking. Analysis of bacterial transcription initiation complexes.

R. Ebright, N. Naryshkin, Q. Dong, 2001, Methods in molecular biology.

High-resolution mapping of nucleoprotein complexes by site-specific protein-DNA photocrosslinking: organization of the human TBP-TFIIA-TFIIB-DNA quaternary complex.

G. Orphanides, D. Reinberg, R. Ebright, 1996, Proceedings of the National Academy of Sciences of the United States of America.

Conversion of a helix-turn-helix motif sequence-specific DNA binding protein into a site-specific DNA cleavage agent.

A. Gunasekera, R. Ebright, Y. Ebright, 1990, Proceedings of the National Academy of Sciences of the United States of America.

Retention of transcription initiation factor sigma(70) in transcription elongation: Single-molecule analysis - eScholarship

T. Laurence, R. Ebright, S. Weiss, 2005 .

Site-specific incorporation of probes into RNA polymerase by unnatural-amino-acid mutagenesis and Staudinger-Bertozzi ligation.

R. Ebright, A. Chakraborty, Abhishek Mazumder, 2015, Methods in molecular biology.

Azide-specific labeling of biomolecules by Staudinger-Bertozzi ligation phosphine derivatives of fluorescent probes suitable for single-molecule fluorescence spectroscopy.

R. Ebright, A. Chakraborty, Y. Ebright, 2010, Methods in enzymology.

Mutational analysis of a transcriptional activation region of the VP16 protein of herpes simplex virus.

R. Ebright, S. M. Sullivan, S. Triezenberg, 1998, Nucleic acids research.

Identification and structural modeling of the chlamydial RNA polymerase omega subunit

R. Ebright, H. Fan, J. Fondell, 2022, bioRxiv.

Structure of the LexA repressor-DNA complex probed by affinity cleavage and affinity photo-cross-linking.

R. Ebright, R. Knegtel, R. Kaptein, 1996, Biochemistry.

The functional subunit of a dimeric transcription activator protein depends on promoter architecture.

R. Ebright, S. Busby, Y. Zhou, 1994, The EMBO journal.

Mechanisms of viral activators.

R. Ebright, S. M. Sullivan, A. Berk, 1998, Cold Spring Harbor symposia on quantitative biology.

Redesign of Rifamycin Antibiotics to Overcome ADP‐Ribosylation‐Mediated Resistance

Joel S. Freundlich, R. Ebright, M. Zimmerman, 2022, Angewandte Chemie.

New target for inhibition of bacterial RNA polymerase: 'switch region'.

R. Ebright, A. Chakraborty, N. Connell, 2011, Current opinion in microbiology.

Transcription activation at Class II CAP‐dependent promoters

R. Ebright, S. Busby, 1993, Molecular microbiology.

Determination of the orientation of a DNA binding motif in a protein-DNA complex by photocrosslinking.

R. Ebright, Y. Ebright, P. S. Pendergrast, 1992, Proceedings of the National Academy of Sciences of the United States of America.

Catabolite gene activator protein (CAP) is not an "acidic activating region" transcription activator protein. Negatively charged amino acids of CAP that are solvent-accessible in the CAP-DNA complex play no role in transcription activation at the lac promoter.

X. Zhang, R. Ebright, Y. Ebright, 1992, The Journal of biological chemistry.

GE23077 binds to the RNA polymerase ‘i’ and ‘i+1’ sites and prevents the binding of initiating nucleotides

R. Ebright, S. Tuske, E. Arnold, 2014, eLife.

Correction to: Salinamide F, new depsipeptide antibiotic and inhibitor of bacterial RNA polymerase from a marine-derived Streptomyces sp.

R. Ebright, David Degen, H. Hassan, 2022, The Journal of antibiotics.

Functionalised bicyclic tetramates derived from cysteine as antibacterial agents.

R. Ebright, A. Maxwell, Alexander Pretsch, 2019, Organic & biomolecular chemistry.

Total Synthesis of Pargamicin A.

R. Ebright, J. D. Del Valle, David Degen, 2022, Organic letters.

Distance-restrained docking of rifampicin and rifamycin SV to RNA polymerase using systematic FRET measurements: developing benchmarks of model quality and reliability.

Jennifer L. Knight, Ronald M Levy, Jayanta Mukhopadhyay, 2005, Biophysical journal.

CHAPTER 7 – Steroid Hormone Action Interpreted from X-Ray Crystallographic Studies

R. Ebright, D. Rohrer, C. Weeks, 1984 .

Mechanism of ATP-dependent promoter melting by transcription factor IIH.

D. Reinberg, R. Ebright, T. Kim, 2000, Science.

Inhibition of Bacterial RNA Polymerase by Streptolydigin: Stabilization of a Straight-Bridge-Helix Active-Center Conformation

A. D. Clark, R. Ebright, S. Tuske, 2005, Cell.

Structural and mechanistic basis of RNA extension in reiterative transcription initiation: RNA slipping without DNA scrunching

R. Ebright, Jared T. Winkelman, Yu Liu, 2021 .

XACT-seq comprehensively defines the promoter-position and promoter-sequence determinants for initial-transcription pausing

Deanne M. Taylor, R. Ebright, Premal Shah, 2019, bioRxiv.

The mechanism of RNA 5′ capping with NAD+, NADH, and desphospho-CoA

Craig D. Kaplan, R. Ebright, I. Barvík, 2016, Nature.

RNA polymerase: structural similarities between bacterial RNA polymerase and eukaryotic RNA polymerase II.

R. Ebright, 2000, Journal of molecular biology.

Activation mutants in yeast RNA polymerase II subunit RPB3 provide evidence for a structurally conserved surface required for activation in eukaryotes and bacteria.

R. Ebright, N. Woychik, Q. Tan, 2000, Genes & development.

Rifamycins do not function by allosteric modulation of binding of Mg2+ to the RNA polymerase active center

R. Ebright, S. Darst, L. Westblade, 2008, Proceedings of the National Academy of Sciences.

Structural basis of Rho-dependent transcription termination

R. Ebright, J. Kaelber, E. Firlar, 2022, bioRxiv.

Structural and mechanistic basis of σ-dependent transcriptional pausing

J. Kinney, R. Ebright, Kyle S. Skalenko, 2022, bioRxiv.

Structure of the DNA-binding and RNA-polymerase-binding region of transcription antitermination factor λQ.

G. Montelione, R. Ebright, S. Vorobiev, 2014, Structure.

Opening and Closing of the Bacterial RNA Polymerase Clamp

Shimon Weiss, Jennifer L. Knight, Rolf Jansen, 2012, Science.

Structures of RNA polymerase-antibiotic complexes.

R. Ebright, E. Arnold, K. Das, 2009, Current opinion in structural biology.

The RNA Polymerase “Switch Region” Is a Target for Inhibitors

Jayanta Mukhopadhyay, Eddy Arnold, Rolf Jansen, 2008, Cell.

Identification and Structural Modeling of the RNA Polymerase Omega Subunits in Chlamydiae and Other Obligate Intracellular Bacteria

R. Ebright, H. Fan, J. Fondell, 2023, mBio.

Structural basis of transcription-translation coupling

R. Ebright, G. Blaha, J. Kaelber, 2020, Science.

Three-dimensional EM structure of an intact activator-dependent transcription initiation complex

R. Ebright, H. Berman, E. Arnold, 2009, Proceedings of the National Academy of Sciences.

Structural and mechanistic basis of reiterative transcription initiation

R. Ebright, J. Kaelber, Jared T. Winkelman, 2021, Proceedings of the National Academy of Sciences.

Transcription initiation at a consensus bacterial promoter proceeds via a ‘bind-unwind-load-and-lock’ mechanism

R. Ebright, A. Kapanidis, Abhishek Mazumder, 2021, eLife.

Transcription initiation at a consensus bacterial promoter proceeds via a “bind-unwind-load-and-lock” mechanism

R. Ebright, A. Kapanidis, Abhishek Mazumder, 2021, bioRxiv.

RNA extension drives a stepwise displacement of an initiation-factor structural module in initial transcription

R. Ebright, Wei Lin, Yu Zhang, 2019, Proceedings of the National Academy of Sciences.

Structural Basis of Transcription Inhibition by Fidaxomicin (Lipiarmycin A3).

R. Ebright, A. Kapanidis, E. Eng, 2018, Molecular cell.

Antibacterial Nucleoside-Analog Inhibitor of Bacterial RNA Polymerase

R. Ebright, G. Facchetti, H. Sahl, 2017, Cell.

Structural Basis of Mycobacterium tuberculosis Transcription and Transcription Inhibition.

Nancy D. Connell, Eddy Arnold, Shengjian Li, 2017, Molecular cell.

Antibacterial nucleoside-analog inhibitor of bacterial RNA polymerase: pseudouridimycin

R. Ebright, G. Facchetti, H. Sahl, 2017, bioRxiv.

Structural basis of Mycobacterium tuberculosis transcription and transcription inhibition

R. Ebright, E. Arnold, N. Connell, 2017, bioRxiv.

Interactions between RNA polymerase and the core recognition element are a determinant of transcription start site selection

Deanne M. Taylor, R. Ebright, Yuanchao Zhang, 2016, Proceedings of the National Academy of Sciences.

Multiplexed protein-DNA cross-linking: Scrunching in transcription start site selection

Deanne M. Taylor, R. Ebright, Y. Zhang, 2016, Science.

Interactions between RNA polymerase and the “core recognition element” counteract pausing

R. Ebright, Y. Zhang, Jared G. Knoblauch, 2014, Science.

The transcription bubble of the RNA polymerase-promoter open complex exhibits conformational heterogeneity and millisecond-scale dynamics: implications for transcription start-site selection.

Shimon Weiss, Yusdi Santoso, Timothy D Craggs, 2013, Journal of molecular biology.

Response of RNA polymerase to ppGpp: requirement for the omega subunit and relief of this requirement by DksA.

R. Ebright, R. Gourse, W. Ross, 2005, Genes & development.

Catabolite activator protein: DNA binding and transcription activation.

D. Swigon, R. Ebright, H. Berman, 2004, Current opinion in structural biology.

Functional Interaction between RNA Polymerase α Subunit C-Terminal Domain and σ70 in UP-Element- and Activator-Dependent Transcription

R. Ebright, Hao Chen, Hong Tang, 2003 .

Fluorescence resonance energy transfer (FRET) in analysis of transcription-complex structure and function.

R. Ebright, A. Kapanidis, Y. Ebright, 2003, Methods in enzymology.

Structural Organization of Bacterial RNA Polymerase Holoenzyme and the RNA Polymerase-Promoter Open Complex

Jennifer L. Knight, R. Ebright, R. Levy, 2002, Cell.

Transcription Activation at Class II CAP-Dependent Promoters: Two Interactions between CAP and RNA Polymerase

R. Ebright, W. Niu, T. Heyduk, 1996, Cell.

Fluorescence anisotropy: rapid, quantitative assay for protein-DNA and protein-protein interaction.

R. Ebright, T. Heyduk, T Heyduk, 1996, Methods in enzymology.

Location, structure, and function of the target of a transcriptional activator protein.

B. Chait, R. Ebright, D. Fenyö, 1994, Genes & development.

Upstream promoter sequences and αCTD mediate stable DNA wrapping within the RNA polymerase–promoter open complex

R. Ebright, C. Rivetti, Ekaterine Kortkhonjia, 2007, EMBO reports.

Transcription Factor B Contacts Promoter DNA Near the Transcription Start Site of the Archaeal Transcription Initiation Complex*

R. Ebright, R. A. Scott, N. Naryshkin, 2004, Journal of Biological Chemistry.

Determinants of RNA polymerase alpha subunit for interaction with beta, beta', and sigma subunits: hydroxyl-radical protein footprinting.

R. Ebright, K. Severinov, T. Heyduk, 1996, Proceedings of the National Academy of Sciences of the United States of America.

Pause sequences facilitate entry into long-lived paused states by reducing RNA polymerase transcription rates

Antony Lee, Carlos J Bustamante, C. Bustamante, 2018, Nature Communications.

Structural basis of transcription antitermination by Qλ: NusA induces refolding of Qλ to form nozzle for RNA polymerase exit channel

R. Ebright, Z. Yin, J. Kaelber, 2022, bioRxiv.

Direct Detection of Abortive RNA Transcripts in Vivo

R. Ebright, Bryce E Nickels, B. Nickels, 2009, Science.

The interaction between σ70 and the β-flap of Escherichia coli RNA polymerase inhibits extension of nascent RNA during early elongation

R. Ebright, K. Severinov, A. Hochschild, 2005 .

The Escherichia coli RNA polymerase alpha subunit: structure and function.

R. Ebright, S. Busby, 1995, Current opinion in genetics & development.

New core promoter element in RNA polymerase II-dependent transcription: sequence-specific DNA binding by transcription factor IIB.

T Lagrange, D. Reinberg, R. Ebright, 1998, Genes & development.

The RNA polymerase II general transcription factors: past, present, and future.

G. Orphanides, D. Reinberg, R. Ebright, 1998, Cold Spring Harbor symposia on quantitative biology.

White Paper: Developing Antimicrobial Drugs for Resistant Pathogens, Narrow-Spectrum Indications, and Unmet Needs

R. Ebright, J. Rex, H. Boucher, 2017, The Journal of infectious diseases.

CAP interacts with RNA polymerase in solution in the absence of promoter DNA

Tomasz Heyduk, Richard H. Ebright, R. Ebright, 1993, Nature.

Blocks in the pseudouridimycin pathway unlock hidden metabolites in the Streptomyces producer strain

R. Ebright, S. Donadio, M. Sosio, 2021, Scientific Reports.

High-specificity DNA cleavage agent: design and application to kilobase and megabase DNA substrates.

R. Ebright, Y. Ebright, P. S. Pendergrast, 1994, Science.

Incorporation of an EDTA-metal complex at a rationally selected site within a protein: application to EDTA-iron DNA affinity cleaving with catabolite gene activator protein (CAP) and Cro.

R. Ebright, Y. Ebright, P. S. Pendergrast, 1992, Biochemistry.

Protein-protein interactions in eukaryotic transcription initiation: structure of the preinitiation complex.

D. Reinberg, R. Ebright, X. Sun, 1996, Proceedings of the National Academy of Sciences of the United States of America.

Artificial Sequence-Specific DNA Binding Peptides: Branched-Chain Basic Regions

R. Ebright, M. Pellegrini, 1996 .

The mechanism of variability in transcription start site selection

R. Ebright, T. Strick, Jared T. Winkelman, 2017, eLife.

Translocation of σ70 with RNA Polymerase during Transcription Fluorescence Resonance Energy Transfer Assay for Movement Relative to DNA

R. Ebright, A. Kapanidis, Y. Ebright, 2001, Cell.

Multiple mechanisms disrupt the let-7 microRNA family in neuroblastoma

John T. Powers, P. Cahan, J. Collins, 2016, Nature.

Structural Basis of Transcription Activation: The CAP-αCTD-DNA Complex

Gary Parkinson, Helen M. Berman, Huanwang Yang, 2002, Science.

The Infectious Diseases Society of America's 10 × '20 Initiative (10 New Systemic Antibacterial Agents US Food and Drug Administration Approved by 2020): Is 20 × '20 a Possibility?

Ronald N. Jones, R. Ebright, G. Nau, 2019, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.

Requirement for two copies of RNA polymerase alpha subunit C-terminal domain for synergistic transcription activation at complex bacterial promoters.

R. Ebright, S. Busby, W. Niu, 2002, Genes & development.

Trajectory of DNA in the RNA polymerase II transcription preinitiation complex.

T Lagrange, D. Reinberg, R. Ebright, 1997, Proceedings of the National Academy of Sciences of the United States of America.

Promoter structure, promoter recognition, and transcription activation in prokaryotes

Richard H. Ebright, R. Ebright, S. Busby, 1994, Cell.

Transcription activation at the Escherichia coli uhpT promoter by the catabolite gene activator protein

R. Ebright, T. Merkel, R. Kadner, 1995, Journal of bacteriology.

Transcription activation at Class II CRP‐dependent promoters: identification of determinants in the C‐terminal domain of the RNA polymerase α subunit

R. Ebright, R. Gourse, S. Busby, 1998, The EMBO journal.

Identification of the target of a transcription activator protein by protein-protein photocrosslinking.

R. Ebright, Y. Ebright, Y. Chen, 1994, Science.

Identification of the functional subunit of a dimeric transcription activator protein by use of oriented heterodimers

R. Ebright, S. Busby, Yuhong Zhou, 1993, Cell.

DNA affinity cleaving analysis of homeodomain-DNA interaction: identification of homeodomain consensus sites in genomic DNA.

A. McMahon, R. Ebright, Y. Ebright, 1994, Proceedings of the National Academy of Sciences of the United States of America.

Conversion of a helix-turn-helix motif sequence-specific DNA binding protein into a site-specific DNA cleavage agent.

A. Gunasekera, R. Ebright, Y. Ebright, 1990, Proceedings of the National Academy of Sciences of the United States of America.

Role of glutamic acid-181 in DNA-sequence recognition by the catabolite gene activator protein (CAP) of Escherichia coli: altered DNA-sequence-recognition properties of [Val181]CAP and [Leu181]CAP.

T. Kunkel, R. Ebright, H. Buc, 1987, Proceedings of the National Academy of Sciences of the United States of America.

Nonradioactive, ultrasensitive site-specific protein–protein photocrosslinking: interactions of α-helix 2 of TATA-binding protein with general transcription factor TFIIA and transcriptional repressor NC2

D. Reinberg, R. Ebright, Y. Ebright, 2008, Nucleic acids research.

Molecular basis of DNA sequence recognition by the catabolite gene activator protein: detailed inferences from three mutations that alter DNA sequence specificity.

R. Ebright, P. Cossart, J. Beckwith, 1984, Proceedings of the National Academy of Sciences of the United States of America.

Single-molecule DNA nanomanipulation: Improved resolution through use of shorter DNA fragments

R. Ebright, A. Revyakin, T. Strick, 2005, Nature Methods.

Functional interaction between RNA polymerase alpha subunit C-terminal domain and sigma70 in UP-element- and activator-dependent transcription.

R. Ebright, Hao Chen, Hong Tang, 2003, Molecular cell.

Open Letter 1: Call for a Full and Unrestricted International Forensic Investigation into the Origins of COVID-19

J. Claverie, R. Ebright, J. Helden, 2021 .

DNA binding specificity and sequence of Xanthomonas campestris catabolite gene activator protein-like protein

R. Ebright, Q. Dong, 1992, Journal of bacteriology.

DNA-binding determinants of the alpha subunit of RNA polymerase: novel DNA-binding domain architecture.

R. Ebright, R. Gourse, N. Assa‐Munt, 1996, Genes & development.

Single-molecule DNA nanomanipulation: detection of promoter-unwinding events by RNA polymerase.

R. Ebright, A. Revyakin, T. Strick, 2003, Methods in enzymology.

Identification of an amino acid–base contact in the GCN4–DNA complex by bromouracil-mediated photocrosslinking

R. Ebright, Y. Ebright, E. Blatter, 1992, Nature.

The catabolite gene activator protein (CAP) is not required for indole-3-acetic acid to activate transcription of the araBAD operon of Escherichia coli K-12

R. Ebright, J. Beckwith, 2004, Molecular and General Genetics MGG.

Determinants of the C-Terminal Domain of the Escherichia coli RNA Polymerase α Subunit Important for Transcription at Class I Cyclic AMP Receptor Protein-Dependent Promoters

Mark S. Thomas, R. Ebright, R. Gourse, 2002, Journal of bacteriology.

Affinity Selection-Mass Spectrometry Identifies a Novel Antibacterial RNA Polymerase Inhibitor.

R. Ebright, Xinwei Sher, David Degen, 2017, ACS chemical biology.

Structural Basis of Transcription Inhibition by CBR Hydroxamidines and CBR Pyrazoles.

R. Ebright, N. Connell, Y. Ebright, 2015, Structure.

The σ70 subunit of RNA polymerase mediates a promoter-proximal pause at the lac promoter

Jayanta Mukhopadhyay, R. Ebright, A. Hochschild, 2004, Nature Structural &Molecular Biology.

Synthesis and evaluation of novel analogues of ripostatins.

R. Ebright, David Degen, Shuang Liu, 2014, Chemistry.

Characterization of the activating region of Escherichia coli catabolite gene activator protein (CAP). II. Role at Class I and class II CAP-dependent promoters.

R. Ebright, T. Merkel, T. Merkel, 1994, Journal of molecular biology.

Structural basis of transcription activation: the CAP-alpha CTD-DNA complex.

R. Ebright, H. Berman, Huanwang Yang, 2002, Science.

Structural basis for cAMP-mediated allosteric control of the catabolite activator protein

R. Ebright, S. Tzeng, C. Kalodimos, 2009, Proceedings of the National Academy of Sciences.

Refinement strategies for protein–nucleic acid complexes

R. Ebright, H. Berman, B. Schneider, 1996 .

DNA sequence determinants for binding of the Escherichia coli catabolite gene activator protein.

A. Gunasekera, R. Ebright, Y. Ebright, 1992, The Journal of biological chemistry.

Transcriptome Complexity in a Genome-Reduced Bacterium

Richard H. Ebright, R. Ebright, R. Gourse, 2009 .

The sigma 70 subunit of RNA polymerase mediates a promoter-proximal pause at the lac promoter.

Jayanta Mukhopadhyay, R. Ebright, A. Hochschild, 2004, Nature structural & molecular biology.

Roles of the Histone H2A-H2B Dimers and the (H3-H4)2Tetramer in Nucleosome Remodeling by the SWI-SNF Complex*

R. Ebright, C. Peterson, L. Boyer, 2000, The Journal of Biological Chemistry.

Massively Systematic Transcript End Readout, "MASTER": Transcription Start Site Selection, Transcriptional Slippage, and Transcript Yields.

Deanne M. Taylor, R. Ebright, Anna Valenti, 2015, Molecular cell.

Identification of the activating region of catabolite gene activator protein (CAP): isolation and characterization of mutants of CAP specifically defective in transcription activation.

R. Ebright, Y. Zhou, X. Zhang, 1993, Proceedings of the National Academy of Sciences of the United States of America.

A single substitution in the putative helix‐turn‐helix motif of the pleiotropic activator PrfA attenuates Listeria monocytogenes virulence

R. Ebright, P. Cossart, A. Klarsfeld, 1996, Molecular microbiology.

Orientation of OmpR monomers within an OmpR:DNA complex determined by DNA affinity cleaving.

R. Ebright, Ann M Stock, N. Denissova, 1999, Journal of molecular biology.

Consensus DNA site for the Escherichia coli catabolite gene activator protein (CAP): CAP exhibits a 450-fold higher affinity for the consensus DNA site than for the E. coli lac DNA site.

A. Gunasekera, R. Ebright, Y. Ebright, 1989, Nucleic acids research.

S-[2-(4-azidosalicylamido)ethylthio]-2-thiopyridine: radioiodinatable, cleavable, photoactivatible cross-linking agent.

R. Ebright, Y. Ebright, Y. Chen, 1996, Bioconjugate chemistry.

RNA Polymerase β′ Subunit: A Target of DNA Binding-Independent Activation

R. Ebright, L. Rothman-Denes, D. Wood, 1997, Science.

Mean DNA bend angle and distribution of DNA bend angles in the CAP-DNA complex in solution.

R. Ebright, A. Kapanidis, Y. Ebright, 2001, Journal of molecular biology.

Structural basis of transcription activation

R. Ebright, Yu Zhang, Yu Feng, 2016, Science.

Bioweapon agents: more access means more risk

R. Ebright, N. Connell, 2002, Nature.

The mechanism of transcription start site selection

R. Ebright, T. Strick, Jared T. Winkelman, 2017, bioRxiv.

Identification of a contact between arginine-180 of the catabolite gene activator protein (CAP) and base pair 5 of the DNA site in the CAP-DNA complex.

X. Zhang, R. Ebright, 1990, Proceedings of the National Academy of Sciences of the United States of America.

Phenyl-azide-mediated photocrosslinking analysis of Cro-DNA interaction.

R. Ebright, Y. Chen, 1993, Journal of molecular biology.

Indirect readout of DNA sequence at the primary-kink site in the CAP-DNA complex: recognition of pyrimidine-purine and purine-purine steps.

Helen M Berman, Catherine L Lawson, R. Ebright, 2006, Journal of molecular biology.

Derivatives of CAP having no solvent-accessible cysteine residues, or having a unique solvent-accessible cysteine residue at amino acid 2 of the helix-turn-helix motif.

A. Gunasekera, X. Zhang, R. Ebright, 1991, Journal of biomolecular structure & dynamics.

Rapid RNA polymerase genetics: one-day, no-column preparation of reconstituted recombinant Escherichia coli RNA polymerase.

R. Ebright, K. Severinov, A. Goldfarb, 1995, Proceedings of the National Academy of Sciences of the United States of America.

One-dimensional sliding assists σ70-dependent promoter binding by Escherichia coli RNA polymerase

W. Roos, E. Peterman, R. Ebright, 2018 .

Structural basis of archaeal FttA-dependent transcription termination

R. Ebright, J. Kaelber, T. Santangelo, 2023, bioRxiv.

Corrected nucleotide sequence of M13mp18 gene III.

R. Ebright, J. Messing, Q. Dong, 1992, Gene.

Escherichia coli RNA polymerase holoenzyme: rapid reconstitution from recombinant alpha, beta, beta', and sigma subunits.

R. Ebright, K. Severinov, A. Goldfarb, 1996, Methods in enzymology.

New target for inhibition of bacterial RNA polymerase: 'switch region'.

R. Ebright, N. Connell, S. Sengupta, 2011, Current opinion in microbiology.

Highly efficient 5 ' capping of mitochondrial RNA with NAD + and NADH by yeast 1 and human mitochondrial RNA polymerase 2 3

R. Ebright, D. Wallace, Smita S. Patel, 2022 .

Crystal structure of Mycobacterium tuberculosis transcription initiation complex(ECF sigma factor L) containing 5nt RNA with 6nt spacer

R. Ebright, David Degen, W. Lin, 2019 .

Characterization of the activating region of Escherichia coli catabolite gene activator protein (CAP). I. Saturation and alanine-scanning mutagenesis.

R. Ebright, Y. Ebright, Yuhong Zhou, 1994, Journal of molecular biology.

Structural basis for cAMP-mediated allosteric control of the catabolite activator protein

R. Ebright, S. Tzeng, C. Kalodimos, 2009, Proceedings of the National Academy of Sciences.

Use of "loss-of-contact" substitutions to identify residues involved in an amino acid-base pair contact: effect of substitution of Gln18 of lac repressor by Gly, Ser, and Leu.

R. Ebright, R. H. Ebright, 1985, Journal of biomolecular structure & dynamics.

Structural basis of Rho-dependent transcription termination

R. Ebright, J. Kaelber, E. Firlar, 2023, Nature.

Waksman Institute Areas of Specialization Sensory Biology Plant Genetics Protein Biochemistry Developmental Biology Molecular Genetics of Leaf Development Computational Bioinformatics Laboratory Plastid Molecular Genetics Molecular Genetics of Meiotic Recombination & Chromosome Segregation Molecular

Kulikowski, R. Ebright, R. Kerstetter, 2022 .

Structures of transcription-translation coupling complexes at each stage of the translation cycle

R. Ebright, Li Li, Chengyuan Wang, 2024, bioRxiv.

Structural basis of RfaH-mediated transcription-translation coupling

R. Ebright, J. Kaelber, Chengyuan Wang, 2023, bioRxiv.