The Metric Structure of Nucleic Acids and the Higher Dimension of Their Constituents

The Metric Structure of Nucleic Acids and the Higher Dimension of Their Constituents

Gennadiy Vladimirovich Zhizhin (Skolkovo, Saint Petersburg, Russia)
DOI: 10.4018/IJCCE.2018070101

Abstract

The purpose of the study is to build a metric model of the structure of a nucleic acid molecule, taking into account the higher dimension of its components, the actual lengths of chemical bonds, and the angles between them. Calculations by the constructed model showed the closeness of the known experimental characteristic parameters of the nucleic acid (helix diameter, period length) and the calculated values of these parameters. The internal degree of freedom of the nucleic acid molecule is revealed: the angle of rotation of the phosphoric acid residue relative to the chemical bond connecting it to the five-carbon sugar molecule. It is established that the value of this angle determines the shape of the nucleic acid molecule. It is claimed that the process of transmission of hereditary information and protein synthesis occurs in a space of high dimensionality in ribosomes.
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Introduction

Deoxyribonucleic acid (DNA), as a chemical substance, it was isolated by Johann Friedrich Micher in 1869 from the remains of cells contained in pus. He singled out a substance that includes nitrogen and phosphorus. When Misher determined that this substance has acid properties, the substance was called nucleic acid (Dahm, 2005). It was proved that DNA is the carrier of genetic information (Oswald, MacLeod, & McCarty, 1944). The structure of the double helix DNA it was proposed by Francis Crick and James Watson in 1953 on the base of the X-ray structural data obtained by Maurice Wilkins and Rosalind Franklin and the “Chargaff rules” according to which in each DNA molecule the strict relationships connecting the quantity of nitrogenous bases of different (Watson, & Crick, 1953a, b). For outstanding contributions to this discovery, Francis Crick, James Watson and Maurice Wilkins were awarded the 1962 Nobel Prize in Physiology or Medicine. Deoxyribonucleic acid (DNA) is a biopolymer, the monomer of which is the nucleotide (Albert, et al., 2002; Butler, 2001). Each nucleotide consists of a phosphoric acid residue attached to sugar deoxyribose, to which one of the four nitrogen bases is attached also. The bases that make up the nucleotides are divided into two groups: purines (adenine [A] and guanine [G]) and pyrimidines (cytosine [C] and thymine [T]) are formed by combined five - and six - membered heterocycles.

Nucleotides are long polynucleotide chains covalently linked. These chains in the overwhelming majority of cases (except for some viruses possessing single - stranded DNA genomes) are combined pairwise by means of hydrogen bonds into a secondary structure, called the double helix (Watson, & Crick, 1953a, b; Berg, Tymoczko, & Stryer 2002). Each base on one of the chains is connected to one definite base on the second chain. This specific binding is called complementary. Purines are complementary to pyrimidines (that is, they are capable of forming hydrogen bonds with them): adenine forms bonds only with thymine, and cytosine - with guanine. In a double helix, chains are also linked by hydrophobic interactions and stacking, which do not depend on the DNA base sequence (Ponnuswamy, Gromiha, 1994). Complementarity of the double helix means that the information contained in one chain is also contained in another chain. Complementarity of the double helix means that the information containing in one chain is contained and another chain. Different base pairs form a different number of hydrogen bonds.

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