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

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.

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.

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

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.

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.

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.

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.

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.

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.

Kim. T.-K.. Ebright. R.. and Reinberg. D. (2000). Mechanism of ATP-dependent promoter melting by transcription factor IIH. Science 288: 1418-1422.

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.