DFT study of adenine–cytosine mismatch in quaternary systems involving DNA bases

Abstract

In the present work, the adenine–cytosine mismatch is theoretically investigated in quaternary systems involving DNA bases. The calculations, in gas phase, are performed at M06-2X/6-311++G(d,p) level. The results indicate that the quaternary systems involving G–C base pair are more stable than those containing A–T. Moreover, in the presence of A–T or G–C base pairs, the absolute values of formation energy in quaternary systems involving imino tautomer of adenine (A*) are higher than those including imino form of cytosine (C*). A comparison between systems having A* indicates that the absolute value of formation energy in quaternary systems increases when A* stacks with pyrimidine bases (C or T). In the case of systems containing C*, this behavior is observed when C* stacks with purine bases (G or A). Similar to binary systems, the quaternary systems involving A*–C thermodynamically prefer to transform their geometries into systems containing A–C*. The base pairs are stabilized by hydrogen bonds. The strength of hydrogen bonds in binary and quaternary systems is also examined using atoms in molecules (AIM) and natural bond orbital (NBO) analyses.