Diffusion along DNA

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. 

The dyad symmetry of the operator sequence is probably important in providing tight binding to two subunits of the symmetric tetrameric protein.11-13 It is also possible that repressor molecules move along DNA chains in a one-dimensional diffusion process, and that the symmetry of the operator site facilitates recognition by a protein moving from either direction.14 15... 

Absolute reaction rates can be affected by molecular diffusion processes that dictate the rates at which collisional encounter complexes occur before reaction. This affect usually shows up in the way reaction rates depend on the physical form of the reactants (gas, liquid, solid, solution, etc.), particularly on concentrations for reactants in gas or hquid phases. Adsorption of reactants onto surfaces can enhance the effective concentrations of reactive species and/or reduce the dimensionahty of the diffusion process. Classic work by Eigen and Richter (14) showed how restricting diffusion to one or two dimensions can dramatically increase potential reaction rates, and this principle has been applied to the kinetics of protein translocation along DNA chains, for example. See References 15 and 16 for more information. 

This is faster than the diffusion-controlled reaction of azide ion with small cations (see Section 3.2.1), probably because, like many proteins which bind to DNA, the enzyme binds non-specifically to DNA and then undergoes one-dimensional diffusion along the DNA polymer. 

It is conceivable that diffusion of kinks, or overdamped solitons, along the DNA could act to relax the FPA with a time dependence similar to that predicted for torsional deformation/31 32) High levels of intercalated dyes would be expected to alter both the equilibrium population of kinks and their mobility along the DNA. Hence, this question is addressed by examining the effect of intercalating dyes on the torsional dynamics. 

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