Abstract: DNA replication, repair and recombination must depend on the interaction with the protein. N-methylacetamide(NMA) is one of the typical units in protein. Taking NMA and the bases in DNA as the stu\|died objects, the interaction properties including geometry, charge distribution and binding energy of these NMA-base complexes were investigated in terms of the ABEEMσπ/MM method and the ab initio MP2 method. The geometry optimizations were performed at the B3LYP/6-311++G(d,p) level. The results of ABEEMσπ/MM and ab initio methods were compared. The results of ABEEMσπ/MM and ab initio methods have good agreement. The order of relative binding ability of interaction between NMA and DNA bases holds: guanine>thymine>cytosine>adenine. The parameters of ABEEMσπ/MM have good transferability. This study provides a solid foundation for the research of interaction between the protein and nucleic acid via the ABEEMσπ/MM model.

Key words: N-Methylacetamide, Base, ab initio MP2, ABEEMσπ/MM, Geometry, Binding energy