The Amazing DNA Macromolecule: Computer Modeling of its 3D Structure and the Diversity of Watson–Crick Conformations in the Duplex

Abstract: The development of ideas about the 3D structure of DNA and the mechanisms of its formation, from the discovery of the double helix to the present day, is considered. Methods of modeling the 3D structure at different steps of the study of the central molecule of life are reviewed. The results of calculations of intra- and intermolecular interactions among macromolecule subunits provide grounds for the discussion of the marvelous expediency in DNA molecular structure and its adaptability to important biological functions. New data about the substantial contribution of the chemically monotonous and conformationally flexible sugar-phosphate backbone to the formation of the sequence-dependent 3D structure of DNA are presented. The conformational diversity of DNA manifests itself in both the formation of duplexes (and even triplexes or quadruplexes) with different base pair geometries and the formation of duplexes with Watson–Crick nucleoside pairs containing local conformations falling into different regions of the torsion angles of the sugar-phosphate backbone, i.e., different conformational classes. According to our calculations, these classes can be divided into two groups. One of them includes local conformations in which torsion angles are close to one of the energy minimums of the isolated elementary repeating fragment, while the second group consists of conformations where one or more of these angles deviate from that of the nearest energy minimum by more than 30°. The patterns of the formation of local 3D structures in these two groups differ significantly. © 2023, Pleiades Publishing, Inc.