Title: Kinetics of Protein-DNA Interactions: First-Passage Analysis,
Abstract: All living systems can function only far away from equilibrium, and for this
reason chemical kinetic methods are critically important for uncovering the
mechanisms of biological processes. Here we present a new theoretical method of
investigating dynamics of protein-DNA interactions, which govern all major
biological processes. It is based on a first-passage analysis of biochemical
and biophysical transitions, and it provides a fully analytic description of
the processes. Our approach is explained for the case of a single protein
searching for a specific binding site on DNA. In addition, the application of
the method to investigations of the effect of DNA sequence heterogeneity, and
the role multiple targets and traps in the protein search dynamics are
discussed.