Are there variations in hydrogen bonding abilities of Watson Crick region and other donor-acceptor sites of nucleobases? An <i>ab initio </i>method of studying proton and metal ion affinities of nucleobases

Abstract

The ability to form intermolecular hydrogen bonds in DNA depends on the donor-acceptor atomic sites present in nucleobases where the formation of a stable Watson Crick type hydrogen bonds (WC) other than non Watson Crick hydrogen bonds (NWC) are generally found . The occurrence of strong hydrogen bond in DNA sequences may be viewed with respect to the donor-acceptor abilities of the atomic sites in nucleobases. The proton and metal ion affinities at different atomic sites of nucleobases have been analyzed for better understanding of the hydrogen bonds in Watson Crick base pairs. There are several significant variations of ion affinities between the Watson Crick sites and other sites of nucleobases; herein proton affinities are high at certain atomic sites within Watson Crick region as well as in other sites. In most metal ion-nucleobase complexes, the metal ion interacts with multiple atomic sites. The proton and metal ion affinities of various sites located in these two regions are found to be different, and the proton can interact preferably at a particular site of nucleobase within the Watson Crick region. These particular sites may control the formation of Watson Crick hydrogen bonds in the sequences. The proton affinities are higher than metal ion affinities. Also, proton interacts with a particular atomic site of nucleobase. Here the proton and metal ion affinities of cytosine (O9) and adenine (N9) in Watson Crick region are significantly higher as compared to those of other sites of these nucleobases. On the other hand, N6 of guanine (NWC) and O1 of thymine (WC) are the most basic sites of these nucleobases. These basic sites may be important in the Watson Crick type base pairing of two prime nucleobases.