BIOPHYSICAL THEORY AND MODELING |
Apparent directional scanning for DNA repair
Tong Zhao 1 and Aaron Dinner 1*
1 University of Chicago
* To whom correspondence should be addressed. E-mail: dinner{at}uchicago.edu.
Submitted on April 11, 2007
Revised on May 8, 2007
Accepted on 15 August 2007
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Abstract |
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Recently it was observed that the DNA repair protein human O6-alkylguanine-DNA alkyltransferase (AGT) repairs lesions at the 5' ends of 70-nucleotide single-stranded DNA roughly three-fold more frequently than lesions at the 3' ends (1). Here, we introduce a coarse-grained model to show how a local asymmetry in binding kinetics (rather than thermodynamics) together with irreversible alkyl transfer can give rise to this apparent bias in sequence scanning. Exploration of the parameter space provides quantitative relationships that can be used to validate the proposed mechanism by gel-based assays.
Key Words:
Master equation, cooperative binding, facilitated diffusion, non-specific binding
