Nucleic Acids Research

The effect of netropsin binding on the electrostatic potential of DNA reactive sites is presented. Calculations are performed for atoms N7 and 06 of guanine, N3 and N7 of adenine of model, 25 base pair long, DNA-netropsin complexes. An important weakening of the potential is found spreading along all the oligonucleotide chain studied. The results are discussed in connection with the inhibitory effect of a related ligand, distamycin A, on DNA methylation. INTRODUCTION Interactions between alkylating agents, many of which are potent carcinogens or/and mutagens, and DNA are intensively studied (for reviews see e.g. 1, 2) and the elucidation of the factors which influence these interactions is important for a better understanding of their nature. A particularly interesting problem, which attracted significant attention recently (see e.g. 3) concerns the possible modulating effect on such interactions of the binding to DNA of different types of groove specific ligands. Such a binding will necessarily result in a modification of the electrostatic properties of DNA active sites. Now, it has been shown in our laboratory (4,5) that these electrostatic properties, in particular the molecular electrostatic potential, are able to account satisfactorily for the evolution of the reactivity of a large number of different types of electrophiles towards the principal reactive sites of DNA. We may thus expect that the evaluation of the effect on this property of the binding of a ligand will contribute to the understanding of the associated modification in the reactivity of DNA. In this paper we wish to present the results of model calculations demonstrating the influence of an important representative of the minor groove binding ligands, netropsin, on the electrostatic potentials of particularly impoi— tant DNA reactive sites : N7 and 06 of guanine and N3 and N7 of adenine. © IRL Press Limited, Oxford, England. 8841 Nucleic Acids Research METHOD The B-DNA models used in our calculations were built from 50 5'-nucleotides, producing 25 base pair oligoners, the geometry of these helices being that of Arnott et al. (6). Two codel sequences were studied, the first containing 25 AT base pairs and the second 5 central AT base pairs surrounded by 10 GC base pairs on each side. A model counterion screening of the nucleic acid segments was performed by placing a magnesium cation at the bridge position (1.99 A from each anionic oxygen) of every second phosphate and out of step in the two phosphodiester chains (7). In this way 25 magnesium cations were positioned, resulting in a total charge on the nucleic acid of +2. The geooetry of netropsin-DNA complex was obtained by the energy minimization technique described in (8). The minimization was done independently for the two sequences studied. In both DNA segments the optimally bound netropsin was located close to the center of the segment, deep in the minor groove, following the results obtained in (8). The molecular electrostatic potentials presented in figs. 1 and 2 represent average values over all the accessible surface of the atoms studied. This technique is described in detail in (9), here we recall only its main features. In order to find the accessible points of an atom within a macromolecule we cover its van der Waals sphere with a grid of uniformly distributed points, generated by the Korobov technique (10). The attacking species, a sphere of a chosen radius, in this case 1.8 A corresponding to CHj (11), is placed in contact with each one of the grid points and it is checked whether the attacking sphere intersects any of the van der Uaals spheres of the other atoms composing the nacromolecule. If no such intersections exist the associated grid point is classed as accessible. For each of these accessible grid points a molecular electrostatic potential is calculated and finally an average value for the atom is obtained. The electrostatic potential is calculated with the use of optimized monopoles, obtained by the Huckel-Del Re procedure, reparametrized (9) to reproduce the electrostatic potentials of the nucleic acid subunits, calculated with the use of Overlap Multipole Expansions (5) derived from ab initio wave functions. Charge redistribution between the subunits was accounted for by calculating the reparanetrized Huckel-Del Re roonopoles for macroeolecular fragments containing centrally the subunits whose charges are desired (9). A net charge of -1 was maintained for a nucleotide to a precision of 0.0004e. RESULTS In f i g . 1 we present the electrostatic potentials calculated for the B-