Award details

Understanding supercoiling-dependent DNA recognition: a combined experimental and computational approach

Reference	BBS/E/J/000CA455
Principal Investigator / Supervisor	Professor Anthony Maxwell
Co-Investigators / Co-Supervisors	Professor David Lawson
Institution	John Innes Centre
Department	John Innes Centre Department
Funding type	Research
Value (£)	149,315
Status	Completed
Type	Institute Project
Start date	01/02/2012
End date	31/01/2015
Duration	36 months

Abstract

The strength and specificity of many DNA-protein interactions is sensitive to DNA supercoiling, to the extent that E. coli has been shown to re-programme its transcriptome by modulating the superhelical state of its genome. However, we still have little understanding of how such control mechanisms operate. Despite the numerous DNA and protein-DNA structures available in the Protein Database, which have shown the importance of DNA structure and flexibility in DNA recognition, there is almost no structural information on supercoiled DNA because this is more difficult to study using traditional methods such as crystallography or NMR. We will develop tools that allow supercoiling-dependent DNA recognition to be studied in a highly controllable way. We will then use these tools to understand the physical principles that underlie supercoiling-dependent DNA recognition, so that it becomes possible to predict supercoiling-dependency in genome-level studies. The methodology uses specially designed small DNA circles whose structure and superhelical state is both predictable and controllable. Physical insight will come from integrated molecular dynamics (MD) simulations. We will employ three tractable systems to test our methodology: 1) DNA minicircles - these have controllable sequences and levels of supercoiling, and are sufficiently small to be amenable to atomistic simulation. 2) DNA triplexes - we aim to measure how DNA triplex formation is affected by supercoiling the DNA circle and to use triplexes as agents to probe and perturb DNA structure. 3) Phage 434 repressor - this is a paradigm example of a genetic switch that is sensitive to changes in DNA supercoiling and topology, which we will use as a model system of DNA-protein interaction to study supercoiling-dependent recognition.

Summary

unavailable

Committee	Not funded via Committee
Research Topics	Microbiology, Structural Biology, Technology and Methods Development
Research Priority	X – Research Priority information not available
Research Initiative	X - not in an Initiative
Funding Scheme	X – not Funded via a specific Funding Scheme

I accept the terms and conditions of use (opens in new window)

export PDF file

back to list new search