Abstract

We have developed methods to site-specifically introduce fluorescent probes at polypeptide C-termini, at polypeptide hexahistidine tags, in DNA, and in RNA, and we are using fluorescence resonance energy transfer to define distances between pairs of fluorescent probes site-specifically introduced into transcription complexes. We are addressing the following issues (1) structural organization of subunits within RNA polymerase (2) extent of wrapping of DNA around RNA polymerase in initiation complexes (3) positions of the template and non-template strands of the transcription bubble in initiation complexes (4) path of the nascent RNA in elongation complexes (5) interactions with regulatory factors and (6) real-time, single-molecule analysis of initiation, elongation, and regulation.

  Funding Agency

Agency
National Institute of Health (NIH)
Institute
National Center for Research Resources (NCRR)
Type
Biotechnology Resource Grants (P41)
Project #
5P41RR001348-20
Application #
6480863
Study Section
Project Start
2001-08-01
Project End
2002-07-31
Budget Start
1997-10-01
Budget End
1998-09-30
Support Year
20
Fiscal Year
2001
Total Cost
$155,764
Indirect Cost

  Institution

Name
University of Pennsylvania
Department
Type
DUNS #
042250712
City
Philadelphia
State
PA
Country
United States
Zip Code
19104

  Publications

Sheth, Rahul A; Arellano, Ronald S; Uppot, Raul N et al. (2015) Prospective trial with optical molecular imaging for percutaneous interventions in focal hepatic lesions. Radiology 274:917-26
Roussakis, Emmanuel; Spencer, Joel A; Lin, Charles P et al. (2014) Two-photon antenna-core oxygen probe with enhanced performance. Anal Chem 86:5937-45
Courter, Joel R; Abdo, Mohannad; Brown, Stephen P et al. (2014) The design and synthesis of alanine-rich ?-helical peptides constrained by an S,S-tetrazine photochemical trigger: a fragment union approach. J Org Chem 79:759-68
Singh, Prabhat K; Kuroda, Daniel G; Hochstrasser, Robin M (2013) An ion's perspective on the molecular motions of nanoconfined water: a two-dimensional infrared spectroscopy study. J Phys Chem B 117:9775-84
Chuntonov, Lev; Ma, Jianqiang (2013) Quantum process tomography quantifies coherence transfer dynamics in vibrational exciton. J Phys Chem B 117:13631-8
Culik, Robert M; Annavarapu, Srinivas; Nanda, Vikas et al. (2013) Using D-Amino Acids to Delineate the Mechanism of Protein Folding: Application to Trp-cage. Chem Phys 422:
Kuroda, Daniel G; Bauman, Joseph D; Challa, J Reddy et al. (2013) Snapshot of the equilibrium dynamics of a drug bound to HIV-1 reverse transcriptase. Nat Chem 5:174-81
Lam, A R; Moran, S D; Preketes, N K et al. (2013) Study of the ?D-crystallin protein using two-dimensional infrared (2DIR) spectroscopy: experiment and simulation. J Phys Chem B 117:15436-43
Kuroda, Daniel G; Singh, Prabhat K; Hochstrasser, Robin M (2013) Differential hydration of tricyanomethanide observed by time resolved vibrational spectroscopy. J Phys Chem B 117:4354-64
Falvo, Cyril; Zhuang, Wei; Kim, Yung Sam et al. (2012) Frequency distribution of the amide-I vibration sorted by residues in amyloid fibrils revealed by 2D-IR measurements and simulations. J Phys Chem B 116:3322-30

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