Biopolymers and cell. 2007; 23 (1): 35 - 44

The binding of actinocin derivative with DNA fragments (Monte Carlo simulation)

A. V. Shestopalova

    The computer simulations of the interaction of DNA fragments and actinocin derivative (ActII) with ligand-target ratio 1:1 and 2:1 were carried out by a Monte Carlo method taking into account water environment. Low-energy molecular structures corresponding to the most probable models of two types of complexes – binding of ActII in minor groove and intercalation of ActII into GC-site with different complex stehiometry were obtained. The energetic and structural parameters of the complex formation were calculated. The stability of investigated complexes was conditioned by Van der Waals and electrostatic interactions as well as by the interaction with a solvent. The water molecules contribute to the stabilization of complexes due to the formation of water bridges between donor-acceptor groups of DNA fragments and ligands. Possible sizes of ActII binding sites in the minor groove were determined. They equaled 3-4 b.p. per the ligand molecule. The sizes of binding sites of intercalating ActII molecules into GC-site are obviously bigger than 4 b.p. per the ligand molecule. The results obtained are in agreement with the experimental data.

Keywords: DNA fragments, actinocin derivative, complexation, Monte Carlo method, size of binding site, hydration, intermolecular interactions.