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Please use this identifier to cite or link to this item:
http://hdl.handle.net/1903/3959
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| Title: | Flexibility and Control of Protein-DNA Loops |
| Authors: | Kahn, Jason D.
Cheong, Raymond
Edelman, Laurence M.
Mehta, Ruchi A.
Morgan, Michael A. |
| Keywords: | Lac repressor
DNA topology
Monte Carlo simulation
Fluorescence resonance energy transfer |
| Issue Date: | Oct-2006 |
| Publisher: | World Scientific Publishing Company |
| Citation: | http://www.worldscinet/brl/brl.shtml |
| Abstract: | Protein-DNA loops are essential for efficient transcriptional repression and activation. The geometry and stability of the archetypal Lac repressor tetramer (LacI)-DNA loop were investigated using designed hyperstable loops containing lac operators bracketing a sequence-directed bend. Electrophoretic mobility shift assays, DNA cyclization, and bulk and single-molecule fluorescence resonance energy transfer (FRET) demonstrate that the DNA sequence controls whether the LacI-DNA loop forms a compact loop with positive writhe or an open loop with little writhe. Monte Carlo methods for simulation of DNA ring closure were extended to DNA loops, including treatment of variable protein hinge angles. The observed distribution of topoisomer products upon cyclization provides a strong constraint on possible models. The experiments and modeling imply that LacI-DNA can adopt a wide range of geometries but has a strong intrinsic preference for an open form. The flexibility of LacI helps explain in v... |
| Description: | Combined research report and review article on our work in DNA looping. Presented at the Asia and Pacific Workshop on Biological Physics, Singapore, July 2006. |
| URI: | http://hdl.handle.net/1903/3959 |
| Appears in Collections: | Chemistry & Biochemistry Research Works
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