A Nonconventional Approach To Supramolecular Formation Dynamics: The Kinetics Of Assembly Of DNA-Bound Porphyrins

R. F. Pasternack
E. J. Gibbs
Peter J. Collings, Swarthmore College
J. C. dePaula
L. C. Turzo
A. Terracina

Abstract

The kinetics of formation of organized assemblies of trans-bis(N-methylpyridinium-4-yl)diphenylporphine (t-H2Pagg) on the surface of calf thymus DNA has been studied via stopped-flow techniques. The reactions show a complicated kinetic profile at both 422 (reactant peak) and 450 nm (product peak), beginning with an apparent induction period followed by a rapid color change whose rate depends on the initial conditions of concentration and ionic strength. The kinetic data can be fit with a closed-form integrated rate law involving four kinetic parameters. A theoretical basis for the form of the integrated rate law is offered in which the formation of an aggregation nucleus is rate determining, a step that is catalyzed by the fractal array of porphyrins produced through the reaction. The process is thus considered to be autocatalytic with two of the parameters (k(o) and k(c)) representing the rate constants for the noncatalytic and catalytic pathways, respectively. The remaining parameters are related to the size of the aggregation nucleus (m) and the growth rate of the catalytic array (n). The dependence of each of these kinetic terms on drug load and salt concentration is described.