Investigation of base pairs containing oxidized guanine using ab initio method and ABEEMσπ polarizable force field

• We have developed the ABEEMσπ polarizable force field.
• The performance of this method is better than those of the common force fields.
• The mutations induced by oxidized guanines have been investigated by this method.
• The accuracy of this method is close to that of the MP2 method.

The integrity of the genetic information is constantly threatened by oxidizing agents. Oxidized guanines have all been linked to different types of cancers. Theoretical approaches supplement the assorted experimental techniques, and bring new sight and opportunities to investigate the underlying microscopic mechanics. Unfortunately, there is no specific force field to DNA system including oxidized guanines. Taking high level ab initio calculations as benchmark, we developed the ABEEMσπ fluctuating charge force field, which uses multiple fluctuating charges per atom. And it was applied to study the energies, structures and mutations of base pairs containing oxidized guanines. The geometries were obtained in reference to other studies or using B3LYP/6-31+G* level optimization, which is more rational and timesaving among 24 quantum mechanical methods selected and tested by this work. The energies were determined at MP2/aug-cc-pVDZ level with BSSE corrections. Results show that the constructed potential function can accurately simulate the change of H-bond and the buckled angle formed by two base planes induced by oxidized guanine, and it provides reliable information of hydrogen bonding, stacking interaction and the mutation processes. The performance of ABEEMσπ polarizable force field in predicting the bond lengths, bond angles, dipole moments etc. is generally better than those of the common force fields. And the accuracy of ABEEMσπ PFF is close to that of the MP2 method. This shows that ABEEMσπ model is a reliable choice for further research of dynamics behavior of DNA fragment including oxidized guanine.

The mutations induced by oxidized guanine (such as 8-oxo-G) using ABEEMσπ fluctuating charge force field, which partitions a molecule into atoms, σ bonds, lone pair electrons, and π bonds. This figure only shows these atoms, σ bonds, and lone pair electrons of 8-oxo-G. Four common oxidized guanines, which are shown in this figure, have been investigated.Figure optionsDownload high-quality image (222 K)Download as PowerPoint slide