Studies of a mispaired DNA recognized by a rhodium intercalator based on the ABEEMσπ/MM method

The mispaired DNA bound by a rhodium intercalator was simulated based on the newly constructed ABEEMσπ/MM fluctuating charge model. The RMSD of atomic coordinates between the simulated structure and crystal structure fell in a range of 0.07–0.14 Å. It indicates that, the present ABEEMσπ/MM method is able to well simulate the system of mispaired DNA and metal complex. Then we studied the recognition of the Δ-[Rh(bpy)2chrysi]3+ [chrysene-5,6-quinone diimine (chrysi)] to DNA double helix including an AC mismatched pair by molecular modeling. The results demonstrate that the present rhodium complex optimally chooses the major groove to recognize the A4C21/A5T20 site next to the AC mismatched pair. In that case, the mismatched C21 is going to flip into the major groove, while the A4 is keeping π-stacked with the chrysi ligand. The hydrogen bonds of A4⋯C21 are broken. The interaction energy between Rh complex and DNA is estimated −410.09 kcal/mol, which is lower than that for the metal complex inserting the DNA at the matched site and mismatched G3C22/A4C21 site of the DNA duplex from the major groove.