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Springer (part of Springer Nature), Biophysical Reviews, 3(8), p. 233-243

DOI: 10.1007/s12551-016-0208-8

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Protein/DNA interactions in complex DNA topologies: expect the unexpected

Journal article published in 2016 by Agnes Noy ORCID, Thana Sutthibutpong, Sarah A. Harris ORCID
This paper is made freely available by the publisher.
This paper is made freely available by the publisher.

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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.