HYDRATE MODEL OF THE EQUILIBRIUM DNA–WATER SYSTEMS

Abstract

A hydrate model for the DNA– H2O system is proposed. For the notions developed, available data on a tendency of H2O molecules to form structured hydrates containing atomic groups, molecules, or atoms housed within the structural cavities formed by H-bonded H2O molecules are used. It is shown that the large and small cavities of the hydrate structure II are in close geometric agreement with N-bases and deoxyribose and with other atomic groups of DNA molecules, respectively. On the basis of the model proposed and with the Watson–Crick base-pairing scheme, the number of pairs of N-bases per helix turn (11.25), the density (1.161 g/cm3), and the helix step (0.567 nm) for the quasi-equilibrium DNA (RNA)–water system are computed, the last value nearly coinciding with the well-known alpha-helix step in the protein secondary structure (5.44 nm). Assumptions on the phenomenology of some stages of mitosis are presented.