The Regular Backbone Of DNA
The chemical structure of DNA is a regular backbone of 2’-deoxyriboses, joined by 3’-5’ phosphodiester bonds (Fig. 2.1). The information carried by the molecule is specified by bases attached to the 1’ position of the deoxyriboses. Four bases are used: the purines adenine and guanine, and the pyrimidines cytosine and thymine. The units of base plus ribose or deoxyribose are called nucleosides, and if phosphates are attached to the sugars, the units are called nucleotides.
The chemical structure of RNA is similar to that of DNA. The backbone of RNA uses riboses rather than 2’-deoxyriboses, and the methyl group on the thymine is absent, leaving the pyrimidine uracil.
Clearly the phosphate-sugar-phosphate-sugar along the backbones of DNA and RNA are regular. Can anything be done to make the informa-tion storage portion of the molecule regular as well? At first glance this seems impossible because the purines and the pyrimidines are different sizes and shapes. As Watson and Crick noticed however, pairs of these molecules, adenine-thymine and guanine-cytosine, do possess regular shapes (Fig. 2.2). The deoxyribose residues on both A-T and G-C pairs are separated by the same distance and can be at the same relative orientations with respect to the helix axis. Not only are these pairs regular, but they are stabilized by strong hydrogen bonds. The A-T pair generally can form two hydrogen bonds and the G-C base pair can form three hydrogen bonds between the respective bases. Finally, the base pairs A-T and G-C can stack via hydrophobic interactions.
Hydrogen bonds can form when a hydrogen atom can be shared by a donor such as an amino group and an acceptor such as a carbonyl group. The hydrogen bonds between the bases of DNA are strong because in all cases the three atoms participating in hydrogen bond formation lie in nearly straight lines. In addition to the familiar Wat-son-Crick pairings of the bases, other interactions between the bases have been observed and are also biologically important. These alterna-tive structures frequently occur in tRNA and also are likely to exist in the terminal structures of chromosomes, called telomeres.
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