Molecular modeling and experimental determination of the structure of C8 -arylguanine modified oligonucleotides that preferentially adopt the Z -DNA conformation

Abstract

Molecular Modeling and Experimental Determination of the Structure of C8-Arylguanine Modified Oligonucleotides that Preferentially Adopt the Z-DNA Conformation Sue Ellen Heavner 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*CGCG 3') (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* = 8phenylguanine, G* = 8-tolylguanine, and G* = 8-hydroxymethylphenylguanine in the B and Z-DNA conformations. We performed quantum mechanical calculations at the B3LYP level with the standard 6-31G* 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.

The effect of C8-arylguanine adducts on B/Z-DNA equilibrium: Implications in aryl hydrazine carcinogenesis

“…The computational studies described below are a continuation of work on the 10mers of unmodified CG, CG 8Ph , CG 8Tol , and CG 8HMPh conducted by Heavner 99,101 and some of these results are reproduced here for comparison purposes. The new studies refer to the CG 8CPh and CG 8MMPh derivatives.…”

C8-Arylguanine Modified Hairpin Oligonucleotides: Synthesis, Conformational Analysis, and Tools for the Investigation of Z-DNA Formation

“…The computational studies require the hairpin oligonucleotides to be built and generally follows the protocol established by Heavner and Gannett. 99 All the parameters for the C8arylguanine modified bases were generated either through the work of Heavner 166 or Vongsutilers 167 and were used in the Amber suite of programs such as xLEAP, sander, ptraj, and MM/PB(GB)SA. The hairpin oligonucleotides were built using the previously constructed (CG)5…”