Richard H. Ebright--Selected Publications

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 Ecoli.  Nature 311, 232-235.

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.

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.

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.

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

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.

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., 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.

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.

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.

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.

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.

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.

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.

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

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.

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.

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.

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.

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. 

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.

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.

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