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Q Rev Biophys. 2012 Aug;45(3):257-99. doi: 10.1017/S0033583512000054. Epub 2012 Jul 31.

Bullied no more: when and how DNA shoves proteins around.

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1
Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030-3411, USA.

Abstract

The predominant protein-centric perspective in protein-DNA-binding studies assumes that the protein drives the interaction. Research focuses on protein structural motifs, electrostatic surfaces and contact potentials, while DNA is often ignored as a passive polymer to be manipulated. Recent studies of DNA topology, the supercoiling, knotting, and linking of the helices, have shown that DNA has the capability to be an active participant in its transactions. DNA topology-induced structural and geometric changes can drive, or at least strongly influence, the interactions between protein and DNA. Deformations of the B-form structure arise from both the considerable elastic energy arising from supercoiling and from the electrostatic energy. Here, we discuss how these energies are harnessed for topology-driven, sequence-specific deformations that can allow DNA to direct its own metabolism.

PMID:
22850561
PMCID:
PMC4866820
DOI:
10.1017/S0033583512000054
[Indexed for MEDLINE]
Free PMC Article
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