The marvelous dna macromolecule: computer modeling of dna 3d structure and diversity of watson-crick duplex conformations

Abstract

The work reviews 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. It tracks the methods of modeling the 3D structure at different stages of the study of the main molecule of life. The discussion underscores a marvelous expedient in DNA molecular structure and its adaptability to important biological functions based on the results of calculations of the intra- and intermolecular interactions of macromolecule subunits. The work presents new data about substantial contribution of chemically monotonous and conformationally flexible sugarphosphate backbone to the formation of sequence-dependent 3D structure of DNA. The diversity of the conformational possibilities of DNA is visible both in the formation of duplexes (as well as triplexes and quadruplexes) with different geometric parameters for base pairs and in the formation of duplexes with Watson-Crick nucleoside pairs containing local conformations corresponding to different regions of the torsion angles of the sugar-phosphate backbone (different conformational classes). Based on our calculations, these classes can be divided into two groups. The first group includes local conformations in which the torsion angles are close to one of energy minima of its isolated elemental repeating fragment, and the second group consists of conformations with one or more of these angles deviating from that of the nearest energy minimum by more than 30°. The regularities of the formation of the local 3D structure of these two groups differ significantly.