KINETICS OF NUCLEIC ACID LARGE LIGAND INTERACTIONS - EXACT MONTE-CARLO TREATMENT AND LIMITING CASES OF REVERSIBLE BINDING

Many ligands, including basic polypeptides, histones, and other proteins bind nonspecifically to DNA in such a way as to render unavailable for further binding several contiguous sites (generally bases or base pairs). An accurate description of the kinetics of such large ligand binding requires a more complex theoretical analysis than does the study of the binding of small ligands to DNA. An exact analytical solution of the problem does not appear feasible. Instead, a Monte Carlo approach is developed which provides an essentially exact numerical solution by simulating the binding experiment using a model one‐dimensional lattice to represent the DNA molecule. For the limiting cases of totally irreversible binding and of instantaneous redistribution of bound ligands along the lattice, relatively simple equations can be written and solved for the binding kinetics. These solutions and their realms of applicability are discussed in some detail. Copyright © 1979 John Wiley & Sons, Inc.