Activation barriers for DNA alkylation by carcinogenic methane diazonium ions

Abstract

Methylation reactions of the DNA bases with the methane diazonium ion, which is the reactive intermediate formed from several carcinogenic methylating agents, were examined. The SN2 transition states of the methylation reactions at N7, N3, and O6 of guanine; N7, N3, and N1 of adenine; N3 and O2 of cytosine; and O2 and O4 of thymine were calculated using the B3LYP density functional method. Solvation effects were examined using the conductor-like polarizable continuum method and the combined discrete/SCRF method. The transition states for reactions at guanine N3, adenine N7, and adenine N1 are influenced by steric interactions between the methane diazonium ion and exocyclic amino groups. Both in the gas phase and in aqueous solution, the methylation reactions at N atoms have transition states that are looser, and generally occur earlier along the reaction pathways than reactions at O atoms. The forming bonds in the transition states in water are 0.03 to 0.13 A shorter than those observed in the gas phase, and the activation energies are 13 to 35 kcal/mol higher. The combined discrete/SCRF solvation energy calculations using base-water complexes with three water molecules yield base solvation energies that are larger than those obtained from the CPCM continuum method, especially for cytosine. Reactivities calculated using barriers obtained with the discrete/SCRF method are consistent with the experimentally observed high reactivity at N7 of guanine.

Model transition states for methane diazonium ion methylation of guanine runs in oligomeric DNA

“…The geometries of the water molecules with respect to the bases are the same as those used in the previous investigation on methylation reactions of free DNA bases. 40 Adding explicit water molecules yields results similar to those obtained for System B in Table 1. The explicit water molecules do not change the ordering of the transition-state energies for N7 or O 6 reactions in the gas phase or in the reaction field.…”

“…19 One of the findings of the earlier investigation of free base reactions is that accurate descriptions of the relative reactivities of alkylation sites on different bases requires consideration of discrete interactions between the reaction system and explicit water molecules. 40 In the present work, explicit water molecules were not included due to the complex nature of the systems considered. However, the effect of this omission is expected to be minimized because all of the reactions examined here involve the same base, guanine.…”

“…An investigation of methylation reactions of the free DNA bases at 10 nucleophilic sites with methane diazonium ions carried out at the B3LYP/6-31 þ G* level show that the transitionstate geometries calculated in the gas phase are very similar to those calculated in the CPCM reaction field. 40 However, solvation has a considerable influence on the activation energies of these reactions. For all reactions, the transition-state energies in the gas phase are lower than the reactant energies.…”

“…Instead, model transition states were used. These were constructed using transition-state geometries calculated for the N7 and O 6 methylation reactions of free guanine in the gas phase and in the reaction field 40 using conductorlike polarizable continuum model (CPCM). 45 This approximation assumes that the local geometry of the transition state of the base at the reaction center in a nucleotide is similar to that of the free base, and that the distortion energies of the B-DNA conformation in the transition states for reactions at guanines in different sites are similar.…”

“…The model transition-state geometries in the oligonucleotides were based on previously reported geometries calculated for the corresponding methylation reactions of free guanine. 40 Here, the local geometries in the oligonucleotide reactions were taken to be the same as those of free guanine. While this investigation of transition states is approximate, it provides more fundamentally sound descriptions of reactivity than descriptions based on the molecular electrostatic potentials or ionization potentials of the reactant oligonucleotides.…”