Quarterly Reviews of Biophysics

Review Article

Bullied no more: when and how DNA shoves proteins around

Jonathan M. Fogga1*, Graham L. Randalla2a3*, B. Montgomery Pettitta2a3, De Witt L. Sumnersa4, Sarah A. Harrisa5 and Lynn Zechiedricha1a2 c1

a1 Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030-3411, USA

a2 Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, TX 77030-3411, USA

a3 Department of Chemistry, University of Houston, Houston, TX 77204-5003, USA

a4 Department of Mathematics, Florida State University, Tallahassee, FL 32306-4510, USA

a5 School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, UK

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.

Correspondence:

c1 Author for correspondence: Lynn Zechiedrich, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030-3411, USA. Tel.: 1 (713) 798-5126; Fax: 1 (713) 798-7375; Email: elz@bcm.edu

Footnotes

* These authors contributed equally to this work.