Mg2+/Ca2+ binding to DNA bases: a quantum chemical method and ABEEMrp/MM fluctuating charge model study
writer：Chun-Yang Yu, Yang Yu, Li-Dong Gong*, Zhong-Zhi Yang
keywords：DNA base,Metal cation,Quantum chemical method,ABEEMrp/MM,Polarizable force field
source：期刊
specific source：Theor. Chem. Acc.131, 1098, 2012.
Issue time：2012年
The interactions of Mg2+ and Ca2+ binding to adenine, cytosine, guanine, and thymine at various binding sites were studied by a high-level quantum chemical method and ABEEMrp/MM fluctuating charge model. The geometries and binding energies of M2+-bases complexes were determined at CCSD(T)/6-311++G(2d,2p)//MP2/6-311++G(2d,2p) level of theory, with the basis set superposition error corrections for the binding energy calculations. In comparison with the ab initio results, an accurate classical metal cation–base interaction potential was constructed and parameterized in terms of ABEEMrp/MM model. It is revealed that Mg2+/Ca2+ prefers to bindwith bases at the bidentate position (between two nitrogen atoms or oxygen and nitrogen atoms in purine and pyrimidine), where the binding energy is the largest. Moreover, the distance between M2+ and the base increases from Mg2+ to Ca2+, while the binding energy of Mg2+–base is greater than that of Ca2+-base. The ABEEMrp/MM potential gives reasonable geometries and binding energies compared with the present quantum chemical calculations, and the overall percentage RMSDs are 1.4 and 1.6% for geometries and binding energies, respectively. Furthermore, the transferability of the parameters of the new potential is validated by investigation of Mg2+/Ca2+ binding to tautomer of bases, and
results from our potential also show quite good consistency with those of MP2/6-311++G(2d,2p)//B3LYP/6-311++G(d,p) method, with the overall percentage RMSDs of 2.2 and 4.7% for geometries and binding energies, respectively. This work will serve as a basis for further investigations of the mechanisms of cation effects on the structure and property of nucleic acids