| Thermal denaturation, circular dichroism, and NMR have been used extensively in conformational studies of oligonucleotides. Molecular modeling has become a powerful, if not essential, complement to these experimental techniques. To study the effects of C8-arylated purine adducts caused by carcinogenic aryl hydrazines we combined the two approaches. Two oligonucleotides were prepared, an unmodified oligonucleotide d(5'CGCGCGCGCG 3') and a C8-phenylguanine modified oligonucleotide d( 5'CGCGCG*CGCG3') (G* = 8-phenylguanine). These oligonucleotides were compared using thermal denaturation, circular dichroism, and NMR. The phenyl modification destabilizes the B DNA form and stabilizes the Z DNA form such that the B:Z ratio is near one under physiological conditions.;Modeling studies were conducted on the modified sequence with G* = guanine, G* = 8-phenylguanine, G* = 8-tolylguanine, and G* = 8-hydroxymethylphenylguanine in the B and ZDNA conformations. We performed quantum mechanical calculations at the B3LYP level with the standard 6-31 G* basis set using Gaussian98, and molecular dynamics simulations and free energy calculations using the suite of programs contained in Amber 6 and 7 with the Cornell 95 force field. New parameters for the modified guanines (G*) have been developed for the Cornell force field. Structural and thermodynamic properties of the DNA molecules are described from the analysis of the trajectories.;The phenyl and tolyl-modified DNA's favored the Z form and the B conformation was preferred by the unmodified and hydroxymethylphenyl-modified oligonucleotides. In those cases where experimental data was available, it was in agreement with the theoretical data. The phenyl-modified models were useful in supporting and providing explanation for the experimental results. In light of recent studies, which show a role for Z DNA in gene expression and cell transformation, Z DNA stabilization by C8-arylguanine formation from aryl hydrazines may be relevant to their role in carcinogenesis. |
