DNA Structure Chains

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1. Introduction

1.1 DNA Structure

DNA is a polymer made of subunits called as nucleotides. Each nucleotide consists of a deoxiribose sugar, a phosphste, and a nitrogenous base (Genetics from Genes to Genomes). Watson and Crick proposed the structure for DNA (shown schematically in Figure 1 a). This is the presence of two polynucleotide strands coiling around a common axis and those strands linked together by a specific hydrogen bond scheme between the purine and pyrimidine bases (Figure 1 b), viz. adenine (A) with thymine (T) and guanine (G) with cytosine (C). The carbon atoms of the deoxyribose sugar are distinguished from atoms of the deoxyribose within the nucleotide base by the use of primed numbers from 1-5. The phosphodieser bonds always form a covalent link between the 3′ carbon of one nucleoside and the 5′ carbon of the following nucleoside. The consistent orientation of the nucleotide building blocks gives a chain overall direction, such that the two ends of a single chain are chemically distinct. At the 5′ end, the sugar of the terminal nucleotide has a free 5′ carbon atom and at the other 3′ end of the chain, it is the 3′ carbon of the final nucleotide that is free (Genetics from Genes to Genomes). In the model, two DNA chains spiral around an axis with the sugar-phosphate backbones on the outside and pairs of bases (one from each chain) meeting in the middle. Although both chains wind around the helix axis in a right-handed sense, chemically one of them runs 5′ to 3′ upward, while the other runs in the opposite direction of 5′ to 3′ downward. In short, the two chains are antiparallel. The base pairs are essentially flat and perpendicular to the helix axis, and the planes of the sugars are roughly perpendicular to the base pairs. As the two chains spiral about the helix axis, they wrap around each other spiral about the helix axis, they wrap around each other once every 10 base pairs, or once every 34Ã… (Genes to genomes). In a space-filling representation of the model, the overall shape is that of a cylinder with a diameter of 20Ã… whose axis is the axis of the double helix. The backbones spiral around the axis like threads on a screw, but because there are two backbones, there are two threads, and these two threads are vertically displaced from each other. This displacement of the backbones generates two grooves, one much wider than the other, that also spiral around the helix axis. Biochemists refer to the wider groove as the major groove and the narrower one as the minor groove. The two chains of double helix are held together by hydrogen bonds between complementary base pairs, A-T and G-C. Since the overall shapes of the two base pairs are quite similar, either pair can fit into the structure at each position along with DNA. Moreover, each base pair can be accommodated in the structure in two ways that are the reverse of each other: an A purine may be on strand 1 with its corresponding T pyrimidine on strand 2 or the T pyrimidine may be on strand 1 and the A purine on strand 2.

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