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
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.
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: email@example.com
* These authors contributed equally to this work.