Ebright, R., Cossart, P., Gicquel-Sanzey, B., and Beckwith, J. (1984) Mutations that alter the DNA sequence specificity of the catabolite gene activator protein of E. coli.  Nature 311, 232-235.

Ebright, R., Cossart, P., Gicquel-Sanzey, B., and Beckwith, J. (1984) Molecular basis of DNA sequence recognition by the catabolite gene activator protein: detailed inferences from three mutations that alter DNA sequence specificity.  Proc. Natl. Acad. Sci. USA 81, 7274-7278.

Ebright, R., Le Grice, S., Miller, J., and Krakow, J. (1985) Analogs of cyclic AMP that elicit the biochemically defined conformational change in catabolite gene activator protein (CAP) but do not stimulate binding to DNA. J. Mol. Biol. 182, 91-107.

Ebright, R. and Beckwith, J. (1985) 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. Mol. Gen. Genet. 201, 51-55.

Ebright, R. (1985) 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. J. Biomol. Struct. Dyn. 3, 281-297.

Ebright, R. (1986) Evidence for a contact between glutamine-18 of lac repressor and base pair 7 of lac operator.  Proc. Natl. Acad. Sci. USA 83, 303-307.

Ebright, R., Wong, J., and Chen L.B. (1986) Binding of 2-hydroxybenzo(a)pyrene to estrogen receptors in rat cytosol. Cancer Res. 46: 2349-2351.

Ebright, R., Kolb, A., Buc, H., Kunkel, T., Krakow, J., and Beckwith, J. (1987) Role of glutamic acid 181 in DNA-sequence recognition by the catabolite gene activator protein (CAP) of Escherichia coli.  Proc. Natl. Acad. Sci. USA 84, 6083-6087.

Ebright, R., Ebright, Y., and Gunasekera, A. (1989) 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.  Nucleic Acids Res. 17, 10295-10305.

Ebright, R., Ebright, Y., Pendergrast, P.S., and Gunasekera, A. (1990) Conversion of a helix-turn-helix motif sequence-specific DNA binding protein into a site-specific DNA cleavage agent.  Proc. Natl. Acad. Sci. USA 87, 2882-2886.

Ebright, R., Gunasekera, A., Zhang, X., Kunkel, T., and Krakow, J. (1990) Lysine 188 of the catabolite gene activator protein (CAP) plays no role in specificity at base pair 7 of the DNA half site.  Nucleic Acids Res. 18, 1457-1464

Zhang, X. and Ebright, R. (1990) 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.  Proc. Natl. Acad. Sci. USA 87, 4717-4721.

Zhang, X. and Ebright, R. (1990) Substitution of two base pairs (one 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.  J. Biol. Chem. 265, 12400-12403.

Gunasekera, A., Ebright, Y. and Ebright, R. (1990) DNA-sequence recognition by CAP:  Role of the adenine N⁶ atom of base pair 6 of the DNA site.  Nucleic Acids Res. 18, 6853-6856.

Zhang, X., Gunasekera, A., Ebright, Y., and Ebright, R. (1991) 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 of CAP.  J. Biomol. Struct. Dyn. 9, 463-473.

Shin, J., Ebright, R., and Dervan, P. (1991) Orientation of the Lac repressor DNA binding domain in complex with the left lac operator half site characterized by affinity cleaving.  Nucleic Acids Res. 19, 5233-5236.

Zhou, Y., Zhang, X., and Ebright, R. (1991) Random mutagenesis of gene-sized DNA molecules by use of PCR with Taq DNA polymerase.  Nucleic Acids Res. 19, 6052.

Ebright, R. (1991) Identification of amino acid-base pair contacts by genetic methods.  Meths. Enzymol. 208, 620-640.

Zhang, X., Zhou, Y., Ebright, Y., and Ebright, R. (1992) 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.  J. Biol. Chem. 267, 8136-8139.

Gunasekera, A., Ebright, Y. and Ebright, R. (1992) DNA-sequence determinants for binding of the Escherichia coli catabolite gene activator protein (CAP).  J. Biol. Chem. 267, 14713-14720.

Dong, Q. and Ebright, R. (1992) DNA binding specificity and sequence of Xanthomonas campestris catabolite gene activator protein-like protein.  J. Bacteriol. 174, 5757-5461.

Ebright, R., Dong, Q., and Messing, J. (1992) Corrected nucleotide sequence of M13mp18 gene III. Gene 114, 81-3.

Blatter, E., Ebright, Y., and Ebright, R. (1992) Identification of an amino acid-base contact in the GCN4-DNA complex by bromouracil-mediated photocrosslinking.  Nature 359, 650-652.

Pendergrast, P.S., Chen, Y., Ebright, Y., and Ebright, R. (1992) Determination of the orientation of a DNA binding motif in a protein-DNA complex by photocrosslinking.  Proc. Natl. Acad. Sci. USA 89, 10287-10291.

Ebright, Y., Chen, Y., Pendergrast, P.S., and Ebright, R. (1992) Incorporation of an EDTA-metal complex at a rationally selected site within a protein: application to EDTA-iron affinity cleaving with catabolite gene activator protein (CAP) and Cro.  Biochem. 31, 10664-10670.

Chen, Y. and Ebright, R. (1993) Phenyl-azide-mediated photocrosslinking analysis of Cro-DNA interaction.  J. Mol. Biol. 230, 453-460.

Ebright, Y., Chen, Y., Ludescher, R., and Ebright, R. (1993) Iodoacetyl-p-phenylenediamine-EDTA: Reagent for high-efficiency incorporation of an EDTA-metal complex at a rationally selected site within a protein.  Bioconj. Chem. 4, 219-225.

Ebright, R. (1993) Transcription activation at class I CAP-dependent promoters.  Mol. Microbiol. 8, 797-802.

Zhou, Y., Zhang, X., and Ebright, R. (1993) Identification of the activating region of CAP: isolation and characterization of mutants of CAP specifically defective in transcription activation.  Proc. Natl. Acad. Sci. USA 90, 6081-6085.

Zhou, Y., Busby, S., and Ebright, R. (1993) Identification of the functional subunit of a dimeric transcription activator protein by use of "oriented heterodimers."  Cell 73, 375-379.

Heyduk, T., Lee, J., Ebright, Y., Blatter, E., Zhou, Y., and Ebright, R. (1993) CAP interacts with RNA polymerase in solution in the absence of promoter DNA.  Nature 364, 548-549.

Shang, Z., Ebright, Y., Iler, N., Pendergrast, P.S., Echelard, Y., McMahon, A., Ebright, R., and Abate, C. (1994) DNA affinity cleaving analysis of homeodomain-DNA interaction: Identification of homeodomain consensus DNA sites in genomic DNA.  Proc. Natl. Acad. Sci. USA 91, 118-122.

Dong, Q., Blatter, E., Ebright, Y., Bister, K., and Ebright, R. (1994) Identification of amino acid-base contacts in the Myc-DNA complex by site-specific bromouracil-mediated photocrosslinking.  EMBO J. 13, 200-204.

Chen, Y., Ebright, Y., and Ebright, R. (1994) Identification of the target of a transcription activator protein by protein-protein photocrosslinking.  Science 265, 90-92.

Pendergrast, P.S., Ebright, Y., and Ebright, R. (1994) High-specificity DNA cleavage agent: design and application to kilobase and megabase DNA substrates.  Science 265, 959-961.

Blatter, E., Ross, W., Tang, H., Gourse, R., and Ebright, R. (1994) Domain organization of RNA polymerase alpha subunit: C-terminal 85 amino acids constitute a domain capable of dimerization and DNA binding.  Cell 78, 889-896.

Zhou, Y., Pendergrast, P.S., Bell, A., Williams, R., Busby, S., and Ebright, R. (1994) The functional subunit of a dimeric transcription activator protein depends on promoter architecture.  EMBO J. 13, 4549-4557.

Niu, W., Zhou, Y., Dong, Q., Ebright, Y., and Ebright, R. (1994) Characterization of the activating region of Escherichia coli catabolite gene activator protein (CAP): I. Saturation and alanine-scanning mutagenesis.  J. Mol. Biol. 243, 595-602.

Zhou, Y., Merkel, T., and Ebright, R. (1994) Characterization of the activating region of Escherichia coli catabolite gene activator protein (CAP): II. Role at Class I and Class II CAP-dependent promoters.  J. Mol. Biol. 243, 603-610.

Busby, S. and Ebright, R. (1994) Promoter structure, promoter recognition, and transcription activation in prokaryotes.  Cell 79, 743-746.

Tang, H., Severinov, K., Goldfarb, A., Fenyo, D., Chait, B, and Ebright, R. (1994) Location, structure, and function of the target of a transcriptional activator protein.  Genes & Development 8, 3058-3067.

Merkel, T., Dahl, J., Ebright, R., and Kadner, R. (1995) Transcription activation at the Escherichia coli uhpT promoter by the catabolite gene activator protein.  J. Bact. 177, 1712-1718.

Ebright, R. and Busby, S. (1995) Escherichia coli RNA polymerase alpha subunit: structure and function.  Curr. Opin. Genet. Development 5, 197-203.

Tang, H., Severinov, K., Goldfarb, A, and Ebright, R. (1995) Rapid RNA polymerase genetics: one-day, no-column preparation of reconstituted recombinant Escherichia coli RNA polymerase.  Proc. Natl. Acad. Sci. USA 92, 4902-4906.

Gaal, T., Ross, W., Blatter, E., Tang, H., Jia, X., Krishnan, V., Assa-Munt, N., Ebright, R., and Gourse, R. (1996) DNA binding determinants of the alpha subunit of RNA polymerase: a novel DNA binding domain architecture.  Genes & Development 10, 16-26.

Tang, H., Sun, X., Reinberg, D. and Ebright, R. (1996) Protein-protein interactions in eukaryotic transcription initiation: structure of the pre-initiation complex.  Proc. Natl. Acad. Sci. USA 93, 1119-1124.

Dumoulin, P., Ebright, R., Knegtel, R., Kaptein, R., Granger-Schnarr, M. and Schnarr, M. (1996) Structure of the LexA-DNA complex probed by affinity cleavage and affinity photocrosslinking.  Biochem. 35, 4279-4286

Ebright, Y., Chen, Y., Kim, Y. and Ebright, R. (1996) S-[2-(4-azidosalicylamido)ethanethio]-2-thiopyridine: radioiodinatable, cleavable photoactivatible crosslinking agent.  Bioconj. Chem. 7, 380-384.

Sheehan, B., Klarsfeld, A., Ebright, R. and Cossart, P. (1996) A single substitution in the putative helix-turn-helix motif of the pleiotropic activator PrfA attenuates Listeria monocytogenes virulence.  Mol. Microbiol. 20, 785-797.

Pellegrini, M. and Ebright, R. (1996) Artificial DNA binding peptides: branched-chain basic regions.  J. Amer. Chem. Soc. 118, 5831-5835.

Parkinson, G., Wilson, C., Gunasekera, A., Ebright, Y., Ebright, R. and Berman, H. (1996) Structure of the CAP-DNA complex at 2.5 Å resolution: a complete picture of the protein-DNA interface.  J. Mol. Biol. 260, 395-408.

Parkinson, G., Gunasekera, A., Vojtechovsky, J., Zhang, X., Kunkel, T., Berman, H. and Ebright, R. (1996) Aromatic hydrogen bond in sequence-specific protein-DNA interaction.  Nature Structl. Biol. 3, 837-841.

Heyduk, T., Heyduk, E., Severinov, K., Tang, H. and Ebright, R. (1996) Determinants of RNA polymerase alpha subunit for interaction with beta and beta' subunits: hydroxyl-radical protein footprinting.  Proc. Natl. Acad. Sci. USA 93, 10162-10166.

Lagrange, T., Kim, T.-K., Orphanides, G. Ebright, Y., Ebright, R., and Reinberg, D. (1996) High-resolution mapping of nucleoprotein complexes by site-specific protein-DNA photocrosslinking: organization of the human TBP-TFIIA-TFIIB-DNA quaternary complex.  Proc. Natl. Acad. Sci. USA 93, 10620-10625.

Tang, H., Kim, Y., Severinov, K., Goldfarb, A., and Ebright, R. (1996) Escherichia coli RNA polymerase holoenzyme: rapid reconstitution from recombinant alpha, beta, beta', and sigma subunits. Meths. Enzymol. 273, 130-134.

Heyduk, T., Ma, Y., Tang, H., and Ebright, R. (1996) Fluorescence anisotropy: rapid, quantitative assay for protein-DNA and protein-protein interaction.  Meths. Enzymol. 274, 492-503.

Niu, W., Kim, Y., Tau, G., Heyduk, and Ebright, R. (1996) Transcription activation at Class II CAP-dependent promoters: two interactions between CAP and RNA polymerase.  Cell 87, 1123-1134.

Busby, S. and Ebright, R. (1997) Transcription activation at Class II CAP-dependent promoters.  Mol. Microbiol. 23, 853-859.

Miller, A., Wood, D., Ebright, R., and Rothman-Denes, L. (1997) RNA polymerase beta': a target for DNA‑binding-independent activation.  Science 275, 1655-1657.

Kim, T.-K., Lagrange, T., Wang, Y.-W., Griffith, J., Reinberg, D., and Ebright, R. (1997) Trajectory of DNA in the RNA polymerase II transcription preinitiation complex.  Proc. Natl. Acad. Sci. USA 94, 12268-12273.

Lagrange, T., Kapanidis, A., Tang, H., Reinberg, D. and Ebright, R. (1998) New core promoter element in RNA-polymerase-II-dependent transcription: sequence-specific DNA binding by transcription factor IIB.  Genes & Development 12, 34-44.

Savery, N., Lloyd, G., Kainz, M., Gaal, T., Ross, W., Ebright, R., Gourse, R. and Busby, S. (1998) Transcription activation at Class II CRP-dependent promoters: identification of determinants in the C-terminal domain of the RNA polymerase alpha subunit  EMBO J.17, 3439-3447.

Sullivan, S., Horn, P., Olson, V., Koop, A., Niu, W., Ebright, R., and Triezenberg, S. (1998) Mutational analysis of the transcriptional activation region of the VP16 protein of herpes simplex virus.  Nucleic Acids Res.  26, 4487-4496.

Harrison-McMonagle, P., Denissova, N., Martinez-Hackert, E., Ebright, R., and Stock, A. (1999) Orientation of OmpR monomers within an OmpR-DNA complex determined by DNA affinity cleaving.  J. Mol. Biol. 285, 555-566.

Estrem, S., Ross, W., Gaal., Chen, Z.W.S., Niu, W., Ebright, R., and Gourse, R. (1999) Bacterial promoter architecture: subsite structure of UP elements and interactions with the carboxyl-terminal domain of RNA polymerase alphasubunit. Genes & Development 13, 2134-2147.

Busby, S. and Ebright, R. (1999) Transcription activation by catabolite activator protein (CAP).  J. Mol. Biol. 293, 199-213.

Tan, Q., Linask, K.L., Ebright, R. and Woychik, N. (2000) Activation mutants in yeast RNA polymerase subunit RPB3 provide evidence for a structurally conserved surface required for activation in eukaryotes and bacteria.  Genes & Development 14, 339-348.

Boyer, L., Shao, X., Ebright, R., and Peterson, C. (2000) Roles of the histone H2A/H2B dimers and (H3/H4)₂ tetramer in nucleosome remodeling by SWI/SNF complex.  J. Biol. Chem. 275, 11545-11552.

Meibom, K., Kallipolitis, B., Ebright, R., and Valentin-Hansen, P. (2000) Identification of the subunit of CRP that functionally interacts with CytR in CRP-CytR-mediated transcriptional repression.  J. Biol. Chem. 275, 12123-12128.

Kim, T.-K., Ebright, R., and Reinberg, D. (2000) Mechanism of ATP-dependent promoter melting by transcription factor IIH.  Science 288, 1418-1421.

Naryshkin, N., Revyakin, A., Kim, Y., Mekler, V., and Ebright, R. (2000) Structural organization of the RNA polymerase-promoter open complex.  Cell 101, 601-611.

Ebright, R. (2000) RNA polymerase: structural similarities between bacterial RNA polymerase and eukaryotic RNA polymerase II.  J. Mol. Biol. 304, 687-698.

Naryshkin, N., Kim, Y., Dong, Q., and Ebright, R. (2001) Site-specific protein-DNA photocrosslinking: analysis of bacterial transcription initiation complexes.  Meths. Mol. Biol. 148, 336-361.

Minakhin, L., Bhagat, S. Brunning, A., Campbell, E., Darst, S., Ebright, R. and Severinov, K. (2001) Bacterial RNA polymerase subunit omega and eukaryotic RNA polymerase subunit RPB6 are sequence, structural, and functional homologs and promote RNA polymerase assembly Proc. Natl. Acad. Sci. USA 98, 892-897.

Mukhopadhyay, J., Kapanidis, A., Mekler, V., Kortkhonjia, E., Ebright, Y., and Ebright, R. (2001) Translocation of sigma⁷⁰ with RNA polymerase during transcription: fluorescence resonance energy transfer assay for movement relative to DNA.  Cell 106, 453-463.

Kapanidis, A., Ebright, Y., Ludescher, R., Chan, S., and Ebright, R. (2001) Mean DNA bend angle and distribution of DNA bend angles in the CAP-DNA complex in solution.  J. Mol. Biol. 312, 453-468.

Chen, S., Vojtechovsky, J., Parkinson, G., Ebright, R., and Berman, H. (2001) Indirect readout of DNA sequence at the primary-kink site in the CAP-DNA complex: I. DNA binding specificity based on energetics of DNA kinking.  J. Mol. Biol. 314, 63-74.

Chen, S., Gunasekera, A., Zhang, X., Kunkel, T., Ebright, R., and Berman, H. (2001) Indirect readout of DNA sequence at the primary-kink site in the CAP-DNA complex: II. Alteration of DNA binding specificity through alteration of DNA kinking.  J. Mol. Biol. 314, 75-82.

Kapanidis, A., Ebright, Y., and Ebright, R. (2001) Site-specific incorporation of fluorescent probes into protein: hexahistidine-tag-mediated fluorescent labeling using (Ni⁺⁺:nitrilotriacetic acid)_n-fluorochrome conjugates.  J. Amer. Chem. Soc. 123, 12123-12125.

Mekler, V., Kortkhonjia, E., Mukhopadhyay, J., Knight, J., Revyakin, A., Kapanidis, A., Niu, W., Ebright, Y., Levy, R., and Ebright, R. (2002) Structural organization of bacterial RNA polymerase holoenzyme and the RNA polymerase-promoter open complex.  Cell 108, 599-614.

Savery, N., Lloyd, G., Busby, S., Thomas, M., Ebright, R., and Gourse, R. (2002) Determinants of the C-terminal domain of the Escherichia coli RNA polymerase alpha subunit important for transcription at Class I cyclic AMP receptor protein-dependent promoters.  J. Bacteriol. 184, 2273-2280.

Benoff, B., Yang, H., Lawson, C., Parkinson, G., Liu, J., Blatter, E., Ebright, Y., Berman, H., and Ebright, R. (2002) Structural basis of transcription activation: the CAP-alphaCTD-DNA complex.  Science  297, 1562-1566.

Lloyd, G., Niu, W., Trebbutt, J., Ebright, R., and Busby, S. (2002) Requirement for two copies of RNA polymerase alpha subunit C-terminal domain for synergistic transcription activation at complex bacterial promoters.  Genes & Development 16, 2557-2565.

Chen, H., Tang, H., and Ebright, R.H. (2003) Functional interaction between RNA polymerase alpha subunit C-terminal domain and sigma⁷⁰ in UP-element- and activator-dependent transcription.  Mol. Cell 11, 1621-1633.

Bayro, M., Mukhopadhyay, J., Swapna, G.V.T., Huang, J., Ma, L.-C., Sineva, E., Dawson, P., Montelione, G., and Ebright, R. (2003) Structure of antibacterial peptide microcin J25: a 21-residue lariat protoknot.  J. Amer. Chem. Soc. 125, 12382-12383.

Revyakin, A., Allemand, J.-F., Croquette, V., Ebright, R., and Strick, T. (2003) Single-molecule DNA nanomanipulation: detection of promoter unwinding events by RNA polymerase.  Meths. Enzymol. 370, 577-598.

Mukhopadhyay, J., Mekler, V., Kortkhonjia, E., Kapanidis, A., Ebright, Y., and Ebright, R. (2003) Fluorescence resonance energy transfer (FRET) in analysis of transcription-complex structure and function.  Meths. Enzymol. 371, 144-159.

Renfrow, M., Naryshkin, N., Lewis, M., Chen, H.-T., Ebright, R., and Scott, R. (2004) Transcription factor B contacts promoter DNA near the transcription start site of the archaeal transcription initiation complex.  J. Biol. Chem. 279, 2825-2831.

Lawson, C., Swigon, D., Murakami, K., Darst, S., Berman, H., and Ebright, R., (2004) Catabolite activator protein (CAP): DNA binding and transcription activation.  Curr. Opin. Structl. Biol. 14, 10-20.

Revyakin, A., Ebright, R., and Strick, T. (2004) Promoter unwinding and promoter clearance by RNA polymerase: Detection by single-molecule DNA nanomanipulation. Proc. Natl. Acad. Sci. USA 101,4776-4780.

Nickels, B., Mukhopadhyay,  J.,  Garrity, S., Ebright, R., and Hochschild, A. (2004) Sigma⁷⁰ mediates a promoter-proximal pause at the lac promoter.  Nature Structl. Mol. Biol.  11, 544-550.

Mukhopadhyay, J., Sineva, E., Knight, J., Levy, R., and Ebright, R. (2004) Antibacterial peptide microcin J25 (MccJ25) inhibits transcription by binding within and obstructing the RNA polymerase secondary channel.  Mol. Cell.  14, 739-751. 

Revyakin, A., Ebright, R.H., and Strick, T. (2005) Single-molecule DNA nanomanipulation: improved resolution through use of shorter DNA fragments.  Nature Meths. 2, 127-138.

Knight, J., Mekler, V., Mukhopadhyay, J., Ebright, R., and Levy, R. (2005) Distance-restrained docking of rifampicin and rifamycin SV to RNA polymerase using systematic FRET measurements: developing benchmarks of model quality and reliability.  Biophys. J.  88, 925-938.

Lee, N.K., Kapanidis, A., Wang, Y., Michalet, X., Mukhopadhyay, J., Ebright, R.H., and Weiss, S. (2005) Accurate FRET measurements within diffusing single biomolecules using alternating-laser excitation.  Biophys. J. 88, 2939-2953.

Nickels, B. Garrity, S., Mekler, V., Minakhin, L., Severinov, K., Ebright, R.H., and Hochschild, A. (2005) Altering the interaction between sigma⁷⁰ and the beta-flap of Escherichia coli RNA polymerase provides evidence for a barrier to the extension of the nascent RNA during early elongation.  Proc. Natl. Acad. Sci USA 102, 4488-4493.

Tuske, S., Sarafianos, S., Wang, X., Hudson, B., Sineva, E., Mukhopadhyay, J., Birktoft, J, Leroy, O., Ismail, S., Clark, A., Dharia, C., Napoli, A., Laptenko, O., Lee, J., Borukhov, S., Ebright, R.,and Arnold, E., (2005) Inhibition of bacterial RNA polymerase by streptolydigin: stabilization of a straight-bridge-helix active-center conformation.  Cell  122, 541-552.

Vrentas, C., Gaal, T., Ross, W., Ebright, R., and Gourse, R. (2005) Response of RNA polymerase to ppGpp: requirement for the omega subunit and relief of this requirement by DksA.  Genes Dev. 19, 2378-2387.

Kapanidis, A., Margeat, E., Laurence, T., Doose, S., Ho, S.O., Mukhopadhyay, J., Kortkhonjia, E., Mekler, V., Ebright, R., and Weiss, S. (2005) Retention of transcription initiation factor sigma⁷⁰ in transcription elongation: single-molecule analysis.  Mol. Cell 20, 347-356.

Margeat, E., Kapanidis, A., Tinnefield, P., Wang, Y., Mukhopadhyay, J., Ebright, R., and Weiss, S. (2006) Direct observation of abortive initiation and promoter escape within immobilized single transcription complexes.  Biophys. J. 20, 347-356.

Napoli, A., Lawson, C., Ebright, R., and Berman, H. (2006)  Indirect readout of DNA sequence at the primary-kink site in the CAP-DNA complex: recognition of pyrimidine-purine and purine-purine steps.  J. Mol Biol. 357, 173-183.

Tadigotla, V., O'Maoileidigh, D., Sengupta, A., Epshtein, V., Ebright, R., Nudler, E., and Ruckenstein, A. (2006) Thermodynamic and kinetic modeling of transcriptional pausing.  Proc. Natl. Acad. Sci. USA 103, 4439-4444.

Popovych, N., Sun, S., Ebright, R., and Kalodimos, C. (2006) Dynamically driven protein allostery.  Nature Structl. Mol. Biol. 13, 831-838.

Revyakin, A., Liu, C., Ebright, R.H. and Strick, T. (2006) Abortive initiation and productive initiation by RNA polymerase involve DNA scrunching. Science 314, 1139-1143.

Kapanidis, A., Margeat, E., Ho, S.O., Kortkhonjia, E., Weiss, S. and Ebright, R. (2006) Initial transcription by RNA polymerase proceeds through a DNA-scrunching mechanism. Science 314, 1144-1147.

Cellai, S., Vannini, N., Naryshkin, N., Kortkhonjia, E., Ebright, R., and Rivetti, C. (2007) Upstream promoter sequences and aCTD mediate stable DNA wrapping within the RNA polymerase open promoter complex.  EMBO Reports 8, 271-278.

Pavlova, O., Mukhopadhyay, J., Sineva, E., Ebright, R.,  and Severinov, K. (2008) Systematic structure-activity analysis of microcin J25 (MccJ25).  J. Biol. Chem. 283, 25589-25595.

Feklistov, A., Mekler, V., Jiang, Q., Westblade,  L., Irschik, H., Jansen, R., Mustaev, A., Darst, S., and Ebright, R. (2008)  Rifamycins do not function by allosteric modulation of binding of Mg²⁺ to the RNA polymerase active center.  Proc. Natl. Acad. Sci. USA 105, 14820-14825.

Mukhopadhyay, J., Das, K., Ismail, S., Koppstein, D., Jang, M., Hudson, B., Sarafianos, S., Tuske, S., Patel, J., Jansen, R., Irschik, H., Arnold, E., and Ebright, R. (2008) The RNA polymerase "switch region" is a target of inhibitors  Cell 135, 295-307.

Kim, Y., Ebright, Y., Goodman, A., Reinberg, D., and Ebright, R. (2008)  Non-radioactive, ultrasensitive site-specific protein-protein photocrosslinking: interactions of a-helix 2 of TATA-binding protein with general transcription factor TFIIA and with transcriptional repressor NC2.  Nucl. Acids Res. 36, 6143-6154.

Naryshkin, N., Druzhinin S., Revyakin, A., Kim, Y., Mekler, V., and Ebright, R. (2009) Static and kinetic site-specific protein-DNA photocrosslinking: analysis of bacterial transcription initiation complexes.  Meths. Mol. Biol. 543, 403-437.

Popovych, N., Tzeng, S.-R., Tonelli, M.,  Ebright_­, R., and Kalodimos, C. (2009) Structural basis of cAMP-mediated allosteric control of the catabolite activator protein,  Proc. Natl. Acad. Sci. USA 106, 6927-6932.

Goldman, S., Ebright, R., and Nickels, B. (2009) Direct detection of abortive RNA transcripts in vivo.  Science 324, 927-928.

Hudson, B., Quispe, J., Lara, S., Kim, Y., Berman, H., Arnold, E., Ebright, R., and Lawson, C. (2009)  Three-dimensional structure of an intact activator-dependent transcription initiation complex.  Proc. Natl. Acad. Sci. USA 106, 19830-19835.

Ho, M., Hudson, B., Das, K., Arnold, E., and Ebright, R. (2009) Structures of RNA polymerase-antibiotic complexes. Curr. Opin. Structl. Biol. 19, 715-723. 

Chakraborty, A., Wang, D., Ebright, Y., and Ebright, R. (2010) Azide-specific labelling of biomolecules by Staudinger-Bertozzi ligation: phosphine derivatives of fluorescent probes suitable for single-molecule fluorescence spectroscopy.  Meths. Enzymol. 472, 19-30.

Grohmann, D., Nagy, J., Chakraborty, A., Klose, D., Fielden, D., Ebright, R., Michaelis, J., and Werner, F. (2011) The initiation factor TFE and the elongation factor Spt4/5 compete for binding to the RNAP clamp during transcription initiation and elongation.  Mol. Cell 43,263-274.

Xiao, Y., Wei, X., Ebright, R., and Wall, D. (2011) Antibiotic production by myxobacteria plays a role in predation. J. Bacteriol. 193, 4626-4633.

Kuznedelov, K., Semenova, E., Knappe, T., Mukahmedjarov, D., Srivastava, A., Chatterjee, S., Ebright, R., Marahiel, M., and Severinov, K. (2011) The antibacterial threaded-lasso peptide capistruin inhibits bacterial RNA polymerase.   J. Mol. Biol. 412, 842-848.

Srivastava, A., Talaue, M., Liu, S., Degen, D., Ebright, R.Y., Sineva, E., Chakraborty, A., Druzhinin, S., Chatterjee, S., Mukhopadhyay, J., Ebright, Y., Zozula, A., Shen, J., Sengupta, S., Niedfeldt, R., Xin, C., Kaneko, T., Irschik, H., Jansen, R., Donadio, S., Connell, N., and Ebright, R. (2011) New target for inhibition of bacterial RNA polymerase: "switch region." Curr. Opin. Microbiol. 14, 532-543.

Chakraborty, A., Wang, D., Ebright, Y., Korlann, Y., Kortkhonjia, E., Kim, T., Chowdhury, S., Wigneshweraraj, S., Irschik, H., Jansen, R., Nixon, B.T., Knight, J., Weiss, S., and Ebright, R. (2012) Opening and closing of the bacterial RNA polymerase clamp.  Science 337, 591-595.

Srivastava, A., Degen, D., Ebright, Y., and Ebright, R. (2012) Frequency, spectrum, and fitness costs of resistance to myxopyronin in Staphylococcus aureus: myxopyronin resistance has non-zero fitness cost.  Antimicrobial Agents Chemother., 56, 6250-6255.

Zhang, Y., Feng, Y., Chatterjee, S., Tuske, S., Ho, M., Arnold, E., and Ebright, R. (2012)  Structural basis of transcription initiation.  Science 338, 1076-1080.

Robb, N., Cordes, T., Hwang, L., Gryte, K., Duchi, D., Craggs, T., Santoso, Y., Weiss, S., Ebright, R., and Kapanidis, A. (2013)  The transcription bubble of the RNA polymerase-promoter open complex exhibits conformational heterogeneity and millisecond-scale dynamics: implications for transcription start-site selection.  J. Mol. Biol. 425, 875–885.

Vorobiev, S., Gensler, Y., Vahedian-Movahed, H., Seetharaman, J., Su, M., Huang, J., Xiao, R., Kornhaber, G., Montelione, G., Tong, L., Ebright, R., and Nickels, B. (2014) Structure of the DNA-binding and RNA-polymerase-binding region of transcription antitermination factor lambdaQ. Structure 22, 485-495. 

Zhang, Y., Degen, D., Ho, M.X., Sineva, S., Ebright, K., Ebright, Y., Mekler, V., Vahedian-Movahed, H., Feng, Y., Yin, R., Tuske, S., Irschik, H., Jansen, R., Maffioli, S., Donadio, S., Arnold, E., and Ebright, R. (2014) GE23077 binds to the RNA polymerase ‘i’ and ‘i+1’ sites and prevents the binding of initiating nucleotides.  eLife 3, e02450.

Degen, D., Feng, Y., Zhang, Y., Ebright, K., Ebright, Y., Gigliotti, M., Vahedian-Movahed, H., Mandal, S., Talaue, M., Connell, N., Arnold, E., Fenical, W., Ebright, R. (2014) Transcription inhibition by the depsipeptide antibiotic salinamide A.  eLife, 3, e02451.

Vvedenskaya, I., Vahedian-Movahed, H., Bird, J., Knoblauch, J., Goldman, S., Zhang, Y., Ebright, R., and Nickels, B. (2014) Interactions between RNA polymerase and the "core recognition element" counteract pausing.  Science 344, 1285-1289.

Tang, W., Liu, S., Degen, D., Ebright, R., Prusov, E.  (2014) Synthesis and evalutaion of novel analogues of ripostatins.  Chemistry  20, 12310-12309.

Chakraborty, A., Mazumder, A., Lin, M., Hasemeyer, A., Xu, Q., Wang, D., Ebright, Y., and Ebright, R. (2015) Site‑specific incorporation of probes into RNA polymerase by unnatural-amino-acid mutagenesis and Staudinger-Bertozzi ligation.  Meths. Mol. Biol.1276, 101-131.

Hassan,H., Degen, D., JangK., Ebright, R., and Fenical, W. (2015) Salinamide F, New depsipeptide antibiotic and inhibitor of bacterial RNA polymerase from a marine-derived Streptomyces sp.  J. Antibiot. 68, 206-209.

Feng, Y., Degen, D., Wang, X., Gigliotti, M., Liu, S., Zhang, Y., Das, D., Michalchuk, T., Ebright, Y.W., Talaue, M., Connell, N., and Ebright, R.H. (2015) Structural basis of transcription inhibition by CBR hydroxamidines and CBR pyrazoles. Structure, 23, 1470-1481.

Vvedenskaya, I., Zhang, Y., Goldman, S., Valenti, A., Visone, V., Taylor, D., Ebright, R., and Nickels, B. (2015) Massively systematic transcript end readout (MASTER): transcription start site selection and transcriptional slippage.  Mol. Cell 60, 953-965.

Winkelman, J., Vvedenskaya, I., Zhang, Y., Zhang, Y., Bird, J., Taylor, D., Gourse, R., Ebright, R., and Nickels, B. (2016) Multiplexed protein-DNA cross-linking: Scrunching in transcription start site selection.  Science 351, 1090-1093.

Vvedenskaya, I., Vahedian-Movahed, H., Zhang, Y., Taylor, D., Ebright, R., and Nickels, B. (2016) Interactions between RNA polymerase and the core recognition element are a determinant of transcription start site selection.  Proc. Natl. Acad. Sci. USA 113, E2899-E290.

Feng, Y., Zhang, Y., and Ebright, R. (2016) Structural basis of transcription activation. Science 352, 1330‑1333.

Bird, J., Zhang, Y., Tian, Y., Panova, N., Barvík, I., Greene, L., Liu, M., Buckley, B., Krásný, L., Lee, J.K., Kaplan, C., Ebright, R., and Nickels, B. (2016) The mechanism of RNA 5′ capping with NAD+, NADH, and desphospho-CoA.  Nature 535, 444-447. 

Walker, S, Degen, D., Nickbarg, E., Carr, D., Soriano, A., Mandal, M., Painter, R., Sheth, P., Xiao, Li., Sher, X., Murgolo, N., Su, J., Olsen, D., Ebright, R., Young, K. (2017) Affinity selection-mass spectrometry identifies a novel antibacterial RNA polymerase inhibitor. ACS Chem. Biol. 12, 1346-1352.

Lin, W., Mandal, S., Degen, D., Liu, Y., Ebright, Y., Li, S., Feng, Y., Zhang, Y., Mandal, S., Jiang, Y., Liu, S., Gigliotti, M., Talaue, M., Connell, N., Das, K., Arnold, E., and Ebright, R. (2017) Structural basis of Mycobacterium tuberculosis transcription and transcription inhibition.. Mol. Cell 166, 169-179.

Maffioli, S., Zhang, Y., Degen, D., Carzaniga, T., Del Gatto, G., Serina, S., Monciardini, P., Mazzetti, C., Guglierame, P., Candiani, G., Chiriac, A.I., Facchetti, G., Kaltofen, P., Sahl, H.-G., Dehò, G., Donadio, S., and Ebright, R.H. (2017) Antibacterial nucleoside-analog inhibitor of bacterial RNA polymerase. Cell 169, 1240-1248.

Bird, J., Nickels, B., Ebright, R.H. (2017) RNA capping by transcription initiation with non-canonical initiating nucleotides (NCINs): determination of relative efficiencies of transcription initiation with NCINs and NTPs. Bio-Protocol 7, e2336.

Boucher, H., Ambrose, P., Chambers, H., Ebright, R.H., Jezek, A., Murray, B., Newland, J., Ostrowsky, B., Rex, J. (2017) Developing antimicrobial drugs for resistant pathogens and unmet needs. J. Infect. Dis. 216, 228-236.

Yu, L., Winkelman, J., Pukhrambam, C., Strick, T., Nickels, B., and Ebright, R. (2017) The mechanism of variability in transcription start site selection. eLife 6, e32038. 

Lin, W., Das, K., Degen, D., Mazumder, A., Duchi, D., Wang, D., Ebright, Y.W., Ebright, R.Y., Sineva, E., Gigliotti, M., Srivastava, A., Mandal, S., Jiang, Y., Liu, Y., Yin, R., Zhang, Z., Eng, E.T., Thomas, D., Donadio, S., Zhang, H., Zhang, C., Kapanidis, A.N., and Ebright, R.H. (2018) Structural basis of transcription inhibition by fidaxomicin (lipiarmycin A3). Mol. Cell 70, 60-71.

Vvedenskaya, I., Bird, J., Zhang, Y., Zhang, Y., Jiao, X., Barvík, I., Krásný, L., Kiledjian, M., Taylor, D., Ebright. R.H., and Nickels, B. (2018) CapZyme-Seq comprehensively defines promoter-sequence determinants for RNA 5' capping with NAD. Mol. Cell 70, 553-564.

Sosio, M., Gaspari, E., Iorio, M., Pessina, S., Medema, M., Bernasconi, A., Simone, M., Maffioli, S., Ebright, R.H., Donadio, S. (2018) Analysis of the pseudouridimycin biosynthetic pathway provides insights into the formation of C-nucleoside antibiotics.. Cell Chem. Biol. 25, 540-549.

Gabizon, R., Lee, A., Vahedian-Movahed, H., Ebright, R.H., and Bustamante, C. (2018) Pause sequences facilitate entry into long-lived paused states by reducing RNA polymerase transcription rates. Nature Comm., 9, 2930.

Duchi, D., Mazumder, A., Malinen, A., Ebright, R., and Kapanidis, A. (2018) The RNA polymerase clamp interconverts dynamically among three states and is stabilized in a partly closed state by ppGpp. Nucl. Acids Res. 14, 7284-7295.

Bird, J., Basu, U., Kuster, D., Ramachandran, A., Grudzien-Nogalska, E., Kiledjian, M., Temiakov, D., Patel, S., Ebright, R.H. and Nickels, B. (2018) Mitochondrial RNA capping: highly efficient 5'-RNA capping with NAD+ and NADH by yeast and human mitochondrial RNA polymerase. eLife, 7, e42179.

Maffioli, S., Sosio, M., Ebright, R.H. and Donadio, S. (2018) Discovery, properties, and biosynthesis of pseudouridimycin, an antibacterial nucleoside analog inhibitor of bacterial RNA polymerase. J. Indust. Microbiol. Technol. 46, 335-343.

Lin, W., Mandal, S., Degen, D., Cho, M., Feng, Y., Das, K., and Ebright, R.H. (2019) Structural basis of ECF-sigma-factor-dependent transcription initiation. Nature Commun. 10, 710.

Panduwawala, T., Iqbal, S., Thompson, A., Christensen, K., Genov, M., Pretsch, A., Pretsch, D., Liu, S., Ebright, R.H., Howells, A., Maxwell, A., and Moloney, M. (2019) Functionalised bicyclic tetramates derived from cysteine as antibacterial agents. Org. Biomol. Chem. 17, 5615-5632.

Talbot, G., Jezek, A., Murray, B., Jones, R., Ebright, R.H., Nau, G., Rodvold, K., Newland, J., and Boucher, H. (2019) The Infectious Diseases Society of America’s 10 × ’20 Initiative (Ten New Systemic Antibacterial Agents FDA-approved by 2020). Clin. Infect. Dis. 69, 1-11.

Yin, Z., Kaelber, J., and Ebright, R.H. (2019) Structural basis of Q-dependent antitermination. Proc. Natl. Acad. Sci. USA 116, 18384-18390.

Ebright, R.H., Werner, F., and Zhang, (2019).RNA polymerase reaches 60: transcription initiation, elongation, termination, and regulation in prokaryotes. J. Mol. Biol. 431, 3946-3946.

Li, L., Molodtsov, V., Lin, W., Ebright, R.H., and Zhang, Y. (2020) RNA extension drives a stepwise displacement of an initiation-factor structural module in initial transcription. Proc. Natl. Acad. Sci. USA 117, 5801-5809.

Mazumder, A., Lin, M., Kapanidis, A., and Ebright, R.H. (2020) Closing and opening of the RNA polymerase trigger loop. Proc. Natl. Acad. Sci. USA 117. 15642-15649.

Winkelman, J., Pukhrambam, C., Vvedenskaya, I., Zhang, Y., Taylor, D., Shah, P., Ebright, R.H., and Nickels, B.E. (2020) XACT-Seq comprehensively defines the promoter-position and promoter-sequence determinants for initial-transcription pausing. Mol. Cell 79, 797-811.

Wang, C., Molodtsov, V., Firlar, E., Kaelber, J., Blaha, G., Su, M., and Ebright, R.H. (2020) Structural basis of transcription-translation coupling. Science 369, 1359-1365.

Iorio, M., Davatgarbenam, S., Serina, S., Criscenzo, P., Zdouc, M., Simone, M., Maffioli, S., Ebright, R.H., Donadio, S., and M. Sosio (2021) Blocks in the pseudouridimcin pathway unlock hidden metabolites in the Streptomyces producer strain. Sci.  Rep. 11, 5827.

Mazumder, A., Wang, A., Uhm, H., Ebright, R.H., and Kapanidis, A. (2020) RNA polymerase clamp conformational dynamics: long-lived states and modulation by crowding, cations, and nonspecific DNA binding. Nucl. Acids Res. 49, 2790-2802.

Skalenko, K., Li, L., Zhang, Y., Vvedenskaya, I., Winkelman, J., Cope, A., Taylor, D., Shah, P., Ebright, R.H., Kinney, J., Zhang, Y., and Nickels, B., (2021) Promoter-sequence determinants and structural basis of primer-dependent transcription initiation in Escherichia coli. Proc. Natl. Acad. Sci. USA 118, e2106388118.

Mazumder, A., Ebright, R.H., and Kapanidis, A. (2021) Transcription initiation at a consensus bacterial promoter proceeds via a "bind-unwind-load-and-lock" mechanism. eLife 10, e70090.

Winkelman, J., Nickels, B., and Ebright, R.H. (2021) The transition from transcription initiation to transcription elongation: start-site selection, initial transcription, and promoter escape. In RNA Polymerases as Molecular Motors, Second Edition,. eds. Landick, R., Wang, J., and Strick, T. (RSC Publishing, Cambridge, UK), pp. 1-24.

Liu, Y., Winkelman, J., Yu, L., Pukhrambam, C., Zhang, Y., Nickels, B., and Ebright, R.H. (2022) Structural and mechanistic basis of reiterative transcription initiation. Proc. Natl. Acad. Sci. USA 119, e2115746119. 

Ma, Z., He, S., Yuan, Y., Zhuang, Z., Liu, Y., Wang, H., Chen, J., Xu, X., Ding, C., Molodtsov, V., Lin, W., Robertson, G., Weiss, W., Pulse, M., Nguyen, P., Duncan, L., Doyle, T., Ebright, R.H., and Lynch, A. (2022) Design, synthesis, and characterization of TNP-2198, a dual-targeted rifamycin-nitroimidazole conjugate with potent activity against microaerophilic and anaerobic bacterial pathogens. J. Med Chem. 65, 4481-4495.

Pukhrambam, C., Molodtsov, V., Kooshkbagh, M., Tareen, A., Vu, H., Skalenko, K., Su, M., Zhou, Y., Winkelman, J., Kinney, J., Ebright, R.H., and Nickels, B. (2022) Structural and mechanistic basis of s‑dependent transcriptional pausing. Proc. Natl. Acad. Sci. USA 119, e2201301119.

Yin, Z., Bird, J., Kaelber, J., Nickels, B., and Ebright, R.H. (2022). In transcription antitermination by Qlambda, NusA induces refolding of Qlambda to form a nozzle that extends the RNA polymerase exit channel. Proc. Natl. Acad. Sci. USA 119, 2205278119.

Lan, T., Ganapathy, U., Sharma, S., Ahn, Y.-M.,  Zimmerman, M., Molodtsov, V., Hegde, P., Gengenbacher, M., Ebright, R.H., Dartois, V., Freundlich, J., Dick, T., and Aldrich, C. (2022) Redesign of rifamycin antibiotics to overcome ADP‑ribosylation-mediated resistance. Angew. Chem. Intl. Ed. 61, e202211498.

Molodtsov, V., Wang, C., Firlar, E., Kaelber, H., and Ebright, R.H. (2023) Structural basis of Rho‑dependent transcription termination. Nature 614, 367–374.

Cheng, A., Wan, D., Ghatak, A, Wang, C., Feng, D., Fondell, J, Ebright, R.H., and Fan, H. (2023) Identification and structural modeling of the chlamydial RNA polymerase omega subunit. mBio 14, e0349922.

Elbatrawi, T., Gerrein, T., Anwar, A., Makwana, K., Degen, D, Ebright, R.H., and Del Valle, J. (2023) Total synthesis of pargamicin A. Organic Letts. 24, 9285-9289.

Anwar, A., Cain, C., Garza, M., Degen, D., Ebright, R.H., and Del Valle, H. (2024) Stabilizing pseudouridimycin: synthesis, RNA-polymerase inhibitory activity, and antibacterial activity of dipeptide‑modified analogues. ChemMedChem, e202300474.

The Atomwise AIMS Program. (2024) AI is a viable alternative to high throughput screening: a 318-target study. Sci. Rep. 14, 7526.