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1 Polish Journal of Chemistry

1 2003

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An ab initio Post SCF Study on Stacking Interactions of 8-Oxo-9-methylguanine with Four Canonical DNA Bases

Cysewski P., Czyżnikowska-Balcerak Z., Szefler B.

Polish Journal of Chemistry

2003

Vol. 77 / nr 10

1287-1300

Stacking properties of 8-oxo-9-methylguanine interacting with all four canonical nucleic acid bases were studied and compared to dimers formed by unmodified guanine. The impact of twist angle and base-base separation distance on the stacked dimers energies were analyzed based on MP2/6-31G*(d=0.25) quantum chemistry and Amber molecular mechanics single point calculations. Besides, solvent affects were taken into account within PCM formalism. Presented data lead to the conclusion that 8-oxo-9-methylguanine has significantly different stacking properties compared to standard guanine. Although the dimers stabilization energies are similar for standard and modified 9-methylguanine structural properties are significantly diverse. The most stable dimers formed by 8-oxo- 9-methyl-G are characterized by different conformations compared to canonical 9- methylguanine. This may lead to complete alteration of stacking abilities. For example, 8-oxo-9-methyl-G if paired with 9-methyl-G exhibits strong stacking repulsion in the twist region, for which 9-methylguanine/9-methylguanine dimer has major attraction. The most stable stacking pair is formed by 8-oxo-9-methylguanine with 9-methylguanine, while the least stable one corresponds to 8-oxo-9-methylguanine/1-methylcytosine and 9-methylguanine/1-methylcytosine pairs. Besides, significant changes of stacked complexes polarities are observed, especially in case of pairs containing methylated pyrimidines. Polarities of dimer formed by two 9-methylated purines are much less sensitive to the environment but dipole moments of 9-methylpurine/1-methylpyrimidine stacking pairs are significantly altered by taking into account solvent effects. The observed differences in stacking properties between standard and modified guanine are related mainly to charge redistribution rather than direct interactions of O8 oxygen. The correlation energies of stacking dimers are very high and are main source of pairs stabilization. Both 9-methylguanine and 8-oxo-9-methylguanine are characterized by similar values of correlation energy.