Protein diffusion along DNA

This of course does not address the issue of the interactions responsible for specific binding of the protein to the required binding site. 

Almost all proteins displace surface water molecules on binding to DNA. This provides a favorable entropic cost to the change in free energy. 

Protein-DNA interaction the role of water as a facilitator References 

Westhof, Structural water bridges in nucleic acids. In Water and Biological Macromolecules (Westhof, E., ed.) (Boca Raton, FL CRC Press, 1993), pp. 226-243. 

Brennan, S. L. Roderick, Y. Takeda, and B. W. Matthews, Protein-DNA conformational changes in the crystal structure of a lambda Cro-operator complex. Proc. Natl. Acad. Sci. USA, 87 (1990), 8165. 

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DNA mediated photoelectron transfer reactions have been demonstrated60 . Binding to DNA assists the electron transfer between the metal-centered donor-acceptor pairs. The increase in rate in the presence of DNA illustrates that reactions at a macromolecular surface may be faster than those in bulk homogeneous phase. These systems can provide models for the diffusion of molecules bound on biological macromolecular surfaces, for protein diffusion along DNA helices, and in considering the effect of medium, orientation and diffusion on electron transfer on macromolecular surfaces. 

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