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We model the way in which polymers bind to DNA and neutralize its charged backbone by analyzing the dynamics of the distribution of gaps along the DNA. We generalize existing theory for irreversible binding to construct deterministic models which include polymer removal, movement along the DNA, and allow for binding with overlaps. We show that reversible binding alters the capacity of the DNA for polymers by allowing the rearrangement of polymer positions over a longer time scale than when binding is irreversible. When the polymers do not overlap, allowing reversible binding increases the number of polymers adhered and hence the charge that the DNA can accommodate; in contrast, when overlaps occur, reversible binding reduces the amount of charge neutralized by the polymers.

Original publication

DOI

10.1103/PhysRevE.74.041918

Type

Journal article

Journal

Phys Rev E Stat Nonlin Soft Matter Phys

Publication Date

10/2006

Volume

74

Keywords

Binding Sites, Computer Simulation, DNA, DNA-Binding Proteins, Linear Models, Models, Chemical, Models, Molecular, Motion, Polymers, Protein Binding, Static Electricity