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Article: Kinetics of Target Site Localization of a Protein on DNA: A Stochastic Approach
- Article from:
- Biophysical Journal
- Article date:
- September 1, 2004
- Author:
CopyrightCopyright Biophysical Society Sep 2004. Provided by ProQuest LLC. (Hide copyright information)
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ABSTRACT
It is widely recognized that the cleaving rate of a restriction enzyme on target DNA sequences is several orders-of-magnitude faster than the maximal one calculated from the diffusion-limited theory. It was therefore commonly assumed that the target site interaction of a restriction enzyme with DNA has to occur via two steps: one-dimensional diffusion along a DNA segment, and long-range jumps coming from association-dissociation events. We propose here a stochastic model for this reaction which comprises a series of one-dimensional diffusions of a restriction enzyme on nonspecific DNA sequences interrupted by three-dimensional excursions in the solution until the target sequence is ...