The objectives of this work are: (1) To use photochemically detected linear dichroism to determine the orientation of the nucleosome dyad axis in the 30-nm chromatin fiber. We will characterize dichroic properties and energy transfer in the UV-induced cleavage of DNA molecules, and in the UV cleavage of DNA molecules substituted with 5-BrU. Chromatin fibers reconstituted from repeated nucleosome positioning sequences will be studied by the photochemically-detected dichroism method. (2) To characterize quantitatively the extent of bending produced in DNA molecules at A-tracts, and to measure possible changes in DNA stiffness and contour length produced by A-tracts and their junctions with adjacent B-DNA segments. The methods used for these experiments will consist primarily of rotational dynamics following electric field pulses, and cyclization kinetics using DNA ligase. (3) To use stopped flow-flash methods to trap transients in the interaction of lac repressor with DNA, enabling measurement of the rate of migration of repressor from one site to another on the same DNA molecule. Tests to distinguish sliding from intramolecular direct transfer will be employed, and a gel electrophoresis method to measure directly the repressor sliding range will be developed. (4) To characterize the structure and dynamic properties of double helical DNA oligonucleotides containing bulge defects as models for frameshift mutagenesis. High resolution NMR methods will be used, and we will compare the interaction of different mutagenic drugs with the bulge-containing molecules. Gel electrophoresis methods will be used to compare the direction and magnitude of DNA bending at the bulge site with A-tract bending.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
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Physical Biochemistry Study Section (PB)
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Yale University
Schools of Arts and Sciences
New Haven
United States
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Xi, Zhiqun; Zhang, Yongli; Hegde, Rashmi S et al. (2010) Anomalous DNA binding by E2 regulatory protein driven by spacer sequence TATA. Nucleic Acids Res 38:3827-33
Huang, Shar-yin N; Crothers, Donald M (2008) The role of nucleotide cofactor binding in cooperativity and specificity of MutS recognition. J Mol Biol 384:31-47
Zhang, Yongli; McEwen, Abbye E; Crothers, Donald M et al. (2006) Statistical-mechanical theory of DNA looping. Biophys J 90:1903-12
Kuznetsov, Serguei V; Sugimura, Sawako; Vivas, Paula et al. (2006) Direct observation of DNA bending/unbending kinetics in complex with DNA-bending protein IHF. Proc Natl Acad Sci U S A 103:18515-20
Sugimura, Sawako; Crothers, Donald M (2006) Stepwise binding and bending of DNA by Escherichia coli integration host factor. Proc Natl Acad Sci U S A 103:18510-4
Wickiser, J Kenneth; Winkler, Wade C; Breaker, Ronald R et al. (2005) The speed of RNA transcription and metabolite binding kinetics operate an FMN riboswitch. Mol Cell 18:49-60
Zhang, Yongli; Xi, Zhiqun; Hegde, Rashmi S et al. (2004) Predicting indirect readout effects in protein-DNA interactions. Proc Natl Acad Sci U S A 101:8337-41
Zhang, Yongli; Crothers, Donald M (2003) Statistical mechanics of sequence-dependent circular DNA and its application for DNA cyclization. Biophys J 84:136-53
Barbic, A; Crothers, D M (2003) Comparison of analyses of DNA curvature. J Biomol Struct Dyn 21:89-97
Zhang, Yongli; Crothers, Donald M (2003) High-throughput approach for detection of DNA bending and flexibility based on cyclization. Proc Natl Acad Sci U S A 100:3161-6

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