Investigation of protonated base pairs between hypoxanthine and DNA bases by MS and MP2 methods

Abstract

Hypoxanthine (I) is the nucleobase of inosine. In this work, we employed second-order Møller-Plesset perturbation(MP2) method to investigate the protonation properties of hypoxanthine(I), adenine(A), cytosine (C), guanine (G), and thymine (T). The order of proton affinity is as follows: cytosine (N 3 and O 2 (N 3 ) side) ≈ guanine (N 7 ) > adenine (N 1 ) > hypoxanthine (N 7 ) > thymine(O 4 (N 3 side)). To compare the stability of protonated base pairs between I and DNA bases, we investigated the collision-induced dissociation (CID) behavior of the pairs using tandem mass spectrometry method. And the full geometry optimization has been performed for the studied complexes by the MP2 method. Based on the CID results and calculated structures, the stability of the protonated base pairs in DNA decreased in the following order: (I:A+H) + > (I:C+H) + > (I:G+H) + > (I+H:T) + . We investigated the protonated base pairs between hypoxanthine (I) and DNA bases using CID and MP2 methods. The results show that the order of the binding strength of protonated base pairs is (I:C+H) + ˃ (I:A+H) + ˃ (I:G+H) + ˃ (I+H:T) + . If we consider the double helix structure of DNA and the binding effect of the skeleton, the stability order of protonated base pairs in DNA is (I:A+H) + > (I:C+H) + > (I:G+H) + > (I+H:T) + .