DOI: 10.1073/pnas.0603557103. Modeling the Lac repressor-operator assembly: The influence of DNA looping on Lac repressor conformation

Modeling the Lac repressor-operator assembly: The influence of DNA looping on Lac repressor conformation

10.1073/pnas.0603557103

Crossref journal-article

Proceedings of the National Academy of Sciences

Proceedings of the National Academy of Sciences (341)

Abstract

Repression of transcription of the Escherichia coli Lac operon by the Lac repressor (LacR) is accompanied by the simultaneous binding of LacR to two operators and the formation of a DNA loop. A recently developed theory of sequence-dependent DNA elasticity enables one to relate the fine structure of the LacR–DNA complex to a wide range of heretofore-unconnected experimental observations. Here, that theory is used to calculate the configuration and free energy of the DNA loop as a function of its length and base-pair sequence, its linking number, and the end conditions imposed by the LacR tetramer. The tetramer can assume two types of conformations. Whereas a rigid V-shaped structure is observed in the crystal, EM images show extended forms in which two dimer subunits are flexibly joined. Upon comparing our computed loop configurations with published experimental observations of permanganate sensitivities, DNase I cutting patterns, and loop stabilities, we conclude that linear DNA segments of short-to-medium chain length (50–180 bp) give rise to loops with the extended form of LacR and that loops formed within negatively supercoiled plasmids induce the V-shaped structure.

Bibliography

Swigon, D., Coleman, B. D., & Olson, W. K. (2006). Modeling the Lac repressor-operator assembly: The influence of DNA looping on Lac repressor conformation. Proceedings of the National Academy of Sciences, 103(26), 9879â9884.

Authors 3

David Swigon (first)
Bernard D. Coleman (additional)
Wilma K. Olson (additional)

References 43 Referenced 113

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Dates

Type	When
Created	19 years, 2 months ago (June 19, 2006, 9:02 p.m.)
Deposited	3 years, 4 months ago (April 12, 2022, 3:47 p.m.)
Indexed	4 weeks, 2 days ago (July 26, 2025, 5:10 a.m.)
Issued	19 years, 1 month ago (June 27, 2006)
Published	19 years, 1 month ago (June 27, 2006)
Published Online	19 years, 1 month ago (June 27, 2006)
Published Print	19 years, 1 month ago (June 27, 2006)

Funders 0

None

BibTeX

@article{Swigon_2006, title={Modeling the Lac repressor-operator assembly: The influence of DNA looping on Lac repressor conformation}, volume={103}, ISSN={1091-6490}, url={http://dx.doi.org/10.1073/pnas.0603557103}, DOI={10.1073/pnas.0603557103}, number={26}, journal={Proceedings of the National Academy of Sciences}, publisher={Proceedings of the National Academy of Sciences}, author={Swigon, David and Coleman, Bernard D. and Olson, Wilma K.}, year={2006}, month=jun, pages={9879–9884} }

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