Richard H. Ebright Professor Rutgers University Department of Chemistry Waksman Institute Busch Campus Piscataway. NJ 08854 (732) 445-5179 FAX - 5735 ebright@ waksman.rutgers.edu Visit Dr. Ebright's Lab!

Structure. mechanism. and regulation of transcription complexes; small-molecule inhibtors of transcription; single-molecule imaging; single-molecule nanomanipulation

Our group is interested in the first step in gene expression: ie.. transcription.

Our objectives are: (i) to understand the structural and mechanistic basis of transcription initiation. (ii) to understand the structural and mechanistic basis of transcription activation. and (iii) to develop low-molecular-weight inhibitors of transcription initiation and transcription activation.

We conduct research on both prokaryotic transcription (Escherichia coli RNA polymerase) and eukaryotic transcription (yeast and human RNA polymerase II). We use genetic. biochemical. biophysical. and combinatorial-chemistry techniques. including photocrosslinking. fluorescence-polarization. fluorescence-energy-transfer. single-molecule imaging. and single-molecule-nanomanipulation techniques developed in this laboratory.

Selected Publications

Goldman SR, Ebright RH, Nickels BE. (2009) Direct detection of abortive RNA transcripts in vivo. Science. 324(5929):927-8.

Naryshkin N, Druzhinin S, Revyakin A, Kim Y, Mekler V, Ebright RH. (2009) Static and kinetic site-specific protein-DNA photocrosslinking: Analysis of bacterial transcription initiation complexes. Methods Mol Biol. 543:403-37.

Popovych N, Tzeng SR, Tonelli M, Ebright RH, Kalodimos CG. (2009) Structural basis for cAMP-mediated allosteric control of the catabolite activator protein. Proc Natl Acad Sci U S A. 106(17):6927-32.

Mukhopadhyay J, Das K, Ismail S, Koppstein D, Jang M, Hudson B, Sarafianos S, Tuske S, Patel J, Jansen R, Irschik H, Arnold E, Ebright RH. (2008) The RNA polymerase "switch region" is a target for inhibitors. Cell. 135(2):295-307.

Kim Y, Ebright YW, Goodman AR, Reinberg D, Ebright RH. (2008) Nonradioactive, ultrasensitive site-specific protein-protein photocrosslinking: interactions of alpha-helix 2 of TATA-binding protein with general transcription factor TFIIA and transcriptional repressor NC2. Nucleic Acids Res. 36(19):6143-54.

Feklistov A, Mekler V, Jiang Q, Westblade LF, Irschik H, Jansen R, Mustaev A, Darst SA, Ebright RH. (2008) Rifamycins do not function by allosteric modulation of binding of Mg2+ to the RNA polymerase active center. Proc Natl Acad Sci U S A. 105(39):14820-5.

Pavlova O, Mukhopadhyay J, Sineva E, Ebright RH, Severinov K. (2008) Systematic structure-activity analysis of microcin J25. J Biol Chem. 283(37):25589-95.

Cellai S, Mangiarotti L, Vannini N, Naryshkin N, Kortkhonjia E, Ebright RH, Rivetti C. (2007) Upstream promoter sequences and alphaCTD mediate stable DNA wrapping within the RNA polymerase-promoter open complex. EMBO Rep. 8(3):271-8.

Kapanidis AN, Margeat E, Ho SO, Kortkhonjia E, Weiss S, Ebright RH. (2006) Initial transcription by RNA polymerase proceeds through a DNA-scrunching mechanism. Science. 314(5802):1144-7.

Revyakin A, Liu C, Ebright RH, Strick TR. (2006) Abortive initiation and productive initiation by RNA polymerase involve DNA scrunching. Science. 314(5802):1139-43.

Popovych N, Sun S, Ebright RH, Kalodimos CG. (2006) Dynamically driven protein allostery.
Nat Struct Mol Biol. 13(9):831-8.

Tadigotla VR. Maoileidigh DO. Sengupta AM. Epshtein V. Ebright RH. Nudler E. Ruckenstein AE. (2006) Thermodynamic and kinetic modeling of transcriptional pausing. Proc Natl Acad Sci U S A. 103(12):4439-44.

Napoli AA. Lawson CL. Ebright RH. Berman HM. (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(1):173-83.

Margeat E. Kapanidis AN. Tinnefeld P. Wang Y. Mukhopadhyay J. Ebright RH. Weiss S. (2006) Direct observation of abortive initiation and promoter escape within single immobilized transcription complexes. Biophys J. 90(4):1419-31.

Kapanidis AN. Margeat E. Laurence TA. Doose S. Ho SO. Mukhopadhyay J. Kortkhonjia E. Mekler V. Ebright RH. Weiss S. (2005) Retention of transcription initiation factor sigma70 in transcription elongation: single-molecule analysis. Mol Cell. 20(3):347-56.

Vrentas CE. Gaal T. Ross W. Ebright RH. Gourse RL. (2005) Response of RNA polymerase to ppGpp: requirement for the omega subunit and relief of this requirement by DksA. Genes Dev. 19(19):2378-87.

Tuske S. Sarafianos SG. Wang X. Hudson B. Sineva E. Mukhopadhyay J. Birktoft JJ. Leroy O. Ismail S. Clark AD Jr. Dharia C. Napoli A. Laptenko O. Lee J. Borukhov S. Ebright RH. Arnold E. (2005)
Inhibition of bacterial RNA polymerase by streptolydigin: stabilization of a traight-bridge-helix active-center conformation. Cell. 122(4):541-52.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.