title: Protein/DNA interactions in complex DNA topologies: expect the unexpected.
abstract: DNA supercoiling results in compacted DNA structures that can bring distal sites into close proximity. It also changes the local structure of the DNA, which can in turn influence the way it is recognised by drugs, other nucleic acids and proteins. Here, we discuss how DNA supercoiling and the formation of complex DNA topologies can affect the thermodynamics of DNA recognition. We then speculate on the implications for transcriptional control and the three-dimensional organisation of the genetic material, using examples from our own simulations and from the literature. We introduce and discuss the concept of coupling between the multiple length-scales associated with hierarchical nuclear structural organisation through DNA supercoiling and topology.
authors.affiliation: Department of Physics, Biological Physical Sciences Institute, University of York, York, YO10 5DD UK.
authors.forename: Agnes
authors.initials: A
authors.lastname: Noy
authors.affiliation: Theoretical and Computational Physics Group, Department of Physics, King Mongkut University of Technology Thonburi, 126 Pracha Uthit Road, Bang Mod, Thung Khru, Bangkok, Thailand 10140.
authors.forename: Thana
authors.initials: T
authors.lastname: Sutthibutpong
authors.affiliation: School of Physics and Astronomy, University of Leeds, 192 Woodhouse Lane, Leeds, UK LS2 9JT ; Astbury Centre for Structural and Molecular Biology, University of Leeds, 192 Woodhouse Lane, Leeds, UK LS2 9JT.
authors.forename: Sarah
authors.identifier: 0000-0002-2812-1651
authors.initials: S
authors.lastname: A Harris
keywords:  DNA structural organisation; Computer simulations; DNA supercoiling; DNA topology; DNA-binding proteins; Thermodynamics