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Kinetics of nonspecific binding reactions of proteins with DNA flexible coils: Site‐based and molecule‐based association reactions
Author(s) -
Mazur Sharlyn J.,
Record M. Thomas
Publication year - 1986
Publication title -
biopolymers
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.556
H-Index - 125
eISSN - 1097-0282
pISSN - 0006-3525
DOI - 10.1002/bip.360250603
Subject(s) - nucleic acid , chemistry , kinetics , dna , molecule , diffusion , chemical kinetics , biophysics , thermodynamics , biochemistry , organic chemistry , physics , quantum mechanics , biology
Domain effects on the pseudo‐first‐order kinetics of the reversible and irreversible association of proteins or other ligands with nucleic acids containing multiple binding sites are treated using the classical reaction‐diffusion equation applied to a spherical cell model of the nucleic acid solution and a diffuse‐sphere model for the nucleic acid chain molecule. Both uniform and Gaussian distributions of chain segments are analyzed. In general, the details of the segment distribution do not have a major effect on the kinetics of association. Domain effects are best examined experimentally by determining the effect of the molecular weight of the nucleic acid on the kinetics of the association reaction. A theoretical framework is presented that permits such data to be analyzed simply. Kinetic studies over a wide range of nucleic acid molecular weights are required in order to separate the contributions of diffusion and reaction to the observed kinetics, and to determine the contributions of site‐based and molecule‐based elements to the rate constants.