The structure of DNA is a double helix, composed of two polynucleotide strands that are coiled about one another in a spiral (3,4). Each polynucleotide strand is held together by phospho-diester bonds linking adjacent deoxyribose moieties. The two polynucleotide strands are held together by a variety of noncova-lent interactions, including lipophilic interactions between adjacent bases and hydrogen-bonding between the bases on opposite strands. The sugar-phosphate backbones of the two complementary strands are antiparallel; that is, they possess opposite chemical polarity. As one moves along the DNA double helix in one direction, the phosphodiester bonds in one strand will be oriented 5'-3', whereas in the complementary strand, the phosphodiester bonds will be oriented 3'-5'. This configuration results in base-pairs being stacked between the two chains perpendicular to the axis of the molecule. The base-pairing is always specific: Adenine is always paired to thymidine, and guanine is always paired to cytosine. This specificity results from the hydrogen-bonding capacities of the bases themselves. Adenine and thymine form two hydrogen bonds, and guanine and cytosine form three hydrogen bonds. The specificity of molecular interactions within the DNA molecule allows one to predict the sequence of nucleotides in one polynucleotide strand if the sequence of nucleotides in the complementary strand is known (24). Although the hydrogen bonds themselves are relatively weak, the number of hydrogen bonds within a DNA molecule results in a very stable molecule that would never spontaneously separate under physiological conditions. There are many possibilities for hydrogen-bonding between pairs of heterocyclic bases. Most important are the hydrogen-bonded basepairs A:T and G:C that were proposed by Watson and Crick in their double-helix structure of DNA (3,24). However, other forms of base-pairing have been described (25,26). In addition, hydrophobic interactions between the stacked bases in the double helix lend additional stability to the DNA molecule.
Three helical forms of DNA are recognized to exist: A, B, and Z (27). The B conformation is the dominate form under physiological conditions. In B DNA, the basepairs are stacked 0.34 nm apart, with 10 basepairs per turn of the right-handed double helix and a diameter of approx 2 nm. Like B DNA, the A conformer is also a right-handed helix. However, A DNA exhibits a larger diameter (2.6 nm), with 11 bases per turn of the helix, and the bases are stacked closer together in the helix (0.25 nm apart). Careful examination of space-filling models of A and B DNA conformers reveals the presence of a major groove and a minor grove (27). These grooves (particularly the minor groove) contain many water molecules that interact favorably with the amino and keto groups of the bases. In these grooves, DNA-binding proteins can interact with specific DNA sequences without disrupting the base-pairing of the molecule. In contrast to the A and B conformers of DNA, Z DNA is a left-handed helix. This form of DNA has been observed primarily in synthetic double-stranded oligonucleotides, especially those with purine and pyrimidines alternating in the polynucleotide strands. In addition, high salt concentrations are required for the maintenance of the Z DNA conformer. Z DNA possesses a minor groove but no major groove, and the minor groove is sufficiently deep that it reaches the axis of the DNA helix. The natural occurrence and potential physiological significance of Z DNA in living cells has been the subject of much speculation. However, these issues with respect to Z DNA have not yet been fully resolved.
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