title: On the mechanical analogue of DNA.
abstract: The creation of mechanical analogues of biological systems is known as a useful instrument that helps to understand better the dynamical mechanisms of the functioning of living organisms. Mechanical analogues of biomolecules are usually constructed for imitation of their internal mobility, which is one of the most important properties of the molecules. Among the different types of internal motions, angular oscillations of nitrous bases are of special interest because they make a substantial contribution to the base pairs opening that in turn is an important element of the process of the DNA-protein recognition. In this paper, we investigate the possibility to construct a mechanical analogue for imitation of angular oscillations of nitrous bases in inhomogeneous DNA. It is shown that the analogue has the form of a mechanical chain of non-identical pendulums that oscillate in the gravitational field of the Earth and coupled by identical springs. The masses and lengths of pendulums, as well as the distances between neighboring pendulums and the rigidity of springs are calculated. To illustrate the approach, we present the result of construction of the mechanical analogue of the fragment of the sequence of bacteriophage T7D.
authors.affiliation: Institute of Cell Biophysics of the Russian Academy of Sciences, Institutskaya str. 3, Pushchino, Moscow Region, 142290, Russian Federation. kind-@mail.ru.
authors.forename: Ludmila
authors.initials: L
authors.lastname: Yakushevich
mesh_terms: D017123:Bacteriophage T7; D001483:Base Sequence; D001696:Biomechanical Phenomena; D004247:DNA / Q000737:chemistry* / Q000378:metabolism*; D055595:Mechanical Phenomena; D008958:Models, Molecular; D009690:Nucleic Acid Conformation
chemical_list: D004247:DNA
keywords: Bacteriophage T7D; Chain of non-identical pendulums; DNA dynamics; Modified sine-Gordon equation; Oscillations of nitrous bases