Zdorevskyi O. Competitive interaction of hydrogen peroxide and water molecules with recognition sites of DNA macromolecule

Сompetitive interaction of hydrogen peroxide (H2O2) and water molecules with nonspecific (phosphate groups of the DNA backbone) and specific (nucleic bases and base pairs) DNA recognition sites is studied. Atomic-atomic potential functions method as well as quantum mechanics are used for the calculations. Complexes consisting of DNA phosphate groups, nucleic bases Adenine (A), Thymine (T), Guanine (G) and Cytosine (C), as well as AT and GC base pairs with H2O2 and H2O molecules are considered. The calculation results showed that hydrogen peroxide molecule can form a complex with DNA phosphate group, which is no less stable and more long-living than a similar complex with water molecule. Specific atomic groups of nucleic bases that are more energetically advantageous for the formation of a stable complex with hydrogen peroxide molecule than with water molecule are found. It has also been shown that there are certain configurations of AT and GC base pairs ('open' and 'stretched') that are stabilized by hydrogen peroxide molecule significantly better than by water molecule. It has been shown that such states can be observed in DNA unzipping experiments using single-molecule micromanipulation techniques. Therefore, these methods can be used to observe experimentally the interaction of hydrogen peroxide molecules with DNA. The formation of such complexes can block the DNA recognition by enzymes and, therefore, block the genetic information transfer processes in cancer cells during ion beam therapy treatment.