Base Pairing in Nucleic Acids: Double Helical Structure of DNA

The most important discovery in molecular biology was the identification of the right-handed double helical structure of DNA, where two linear chains are held together by base pair complementarity. This discovery by Watson and Crick in 1953 heralded the era of molecular biology, which was preceded by the rapid accumulation of genetic evidence indicating that DNA, as the genetic material of all organisms, is the primary storehouse of all their information. Exceptions to this fundamental principle were found in certain bacterial, plant, and mammalian viruses, in which RNA constitutes the genome. However, the viruses are obligate parasites and are not able to self-propagate as independent species; thus, they have to depend on their hosts, which have DNA as their genetic material. Thus, DNA in all genomes (except some single-stranded DNA viruses) consists of two strands of polydeoxynucleotides which are anti-parallel in respect to the orientation of the 5´-3´ phosphodiester bond in the polymers (Fig. 1D). The two strands are held together by H-bonding between a purine in one strand and a pyrimidine in the complementary strand. Normally, adenine (A) pairs with T and G pairs with C; A and T are held together by two H-bonds, and G and C are held together by three H-bonds involving both exocyclic C O and ring NH (Fig. 1C). As a result, G<img src="../images/7-img-black-circle.jpg" width="7" height="9" />C pairs are more stable than AT pairs. Because U is structurally nearly identical to T, except for the C-5 methyl group, U also pairs with A in the common configuration. Although H-bonds are inherently weak, the stacking of bases in two polynucleotide chains makes the duplex structure of DNA quite stable and induces a fibrillar nature in theDNApolymer. X-ray diffraction studies of the DNA fiber, and subsequent crystallographic studies of small (oligonucleotide) DNA pieces, led to the detailed structural elucidation. This was initially aided by chemical analysis showing equivalence of purines and pyrimidines in all double-stranded DNA and equimolar amounts of A and T and of G and C (Chargaff’s rule), unlike in RNA, which is single stranded (except in some viruses). X-ray diffraction studies also showed that DNA in double helix exists in the B-form, which is right handed and has a wide major groove and a narrow minor groove. Most of the reactive sites in the bases, including C O and NH groups, are exposed in the major groove (Figs. 1C and 1D). One turn of the helix has10 base pairs (bp) with a rise of 34°. Thus, each pair is rotated 36° relative to its neighbor. Elucidation of the structure of DNA bound to proteins show that one turn of the helix containing 10.5 bp could be significantly bent or distorted. For example, some DNA binding proteins bind to the minor groove, causing its widening accompanied by compression of the major groove. In some special regions of the genomes, e.g., in telomeres and segments with unusual repeated sequences, alternative forms such as triple helical structure and Z-DNA may exist. The Z-DNA has a left-handed, double-helical structure. In these or in torsionally stressed DNA, the bases can be held together by different type of H-bonding called Hoogsteen base pairing.