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11. Nucleic Acids

For an excellent summary of high resolution work on nucleic acid fragments see Dickerson, R. E., Drew, H. R., Conner, B. N., Wing, R. M., Fratini, A. V. and Kopka, M. L., Science 216 (1982) 475. This article contains many useful illustrations. See also Drew, H. R. and Dickerson, R. E., J. Mol. Biol . 152 (1981) 723 and Dickerson, R. E. and Drew, H. R., J. Mol. Biol . 149 (1981) 761.

The elucidation of the double-helical nature of DNA was a fundamental step forward in our understanding of the function of DNA. This helicity was deduced from an X-ray diffraction photograph of fibres of DNA taken by Rosalind Franklin (Franklin, R. E., and Gosling, R., Nature 171 (1953) 740; Watson, J. D. and Crick, F. Nature 171 (1953) 737). An analysis of this photograph, expecially if a model of DNA is also available, illustrates some of the principles of diffraction. Since there is the usual reciprocal relationship between distances on the photograph and distances in real space the photograph may be analysed as follows: the very heavy black regions at the top and bottom indicate that the bases stack 3.4 Å apart, perpendicular to the helix axis. The helicity is indicated by the series of diffuse spots in a cross-like pattern in the centre of the photograph. From this follows the distance between points on the helix and its pitch (angle). More recently the double helix has been seen at atomic resolution via the crystal structures of portions of nucleic acids. Thus DNA consists of two polymeric chains twisted around each other in the form of a regular double helix, 20 Å diameter, which makes a complete helical turn every 34 Å. The `backbone' of the helix consists of sugars linked by phosphate groups. Bases (the pyrimidines, thymine and cytosine, and the purines, adenine and guanine) are linked to the sugars and lie to the centre of the double helix. The two chains are joined by hydrogen bonds between these bases. Adenine is paired with thymine and guanine with cytosine. Thus the two strands are complementary, not identical, and proceed in opposite directions along the helix.

Three major types of helices, A, B and Z have been observed in the structures of small polynucleotides [A (Shakked, Z., Rabinovich, D., Cruse, W. B. T., Egert, E., Kennard, O., Sala, G., Salisbury, S. A. and Viswamitra, M. A., Proc. Roy. Soc. B . 213 (1981) 479), B (Wing, R. M., Drew, H. R., Takano, T., Broka, C., Tanake, S., Itakura, K. and Dickerson, R. E., Nature 287 (1980) 755), Z (Wang, A. H.-J., Quigley, G. C., Kolpak, F. J., Crawford, J. L., van Boom, J. H., van der Marel, G. and Rich, A., Nature 282 (1979) 680)].

The normal form of DNA at high humidity is B-DNA. RNA cannot form a B-helix because the oxygen atom O2$^\prime$ interferes with the formation of this. It forms an A-helix. DNA can have both the A and B conformation. RNA-DNA hybrids are always A-type. The B-helix is narrow with no space in the middle, the bases are perpendicular to the helix axis, and there are wide and narrow grooves. In the A-helix the bases are more tilted, there is space in the middle of the helix and the grooves are more nearly the same size. Two conformers of the sugar pucker are found. C2$^\prime$ endo, found in B-DNA, has C2$^\prime$ on the same side of the ring as O5$^\prime$. C2$^\prime$ endo, found in RNA, has C3$^\prime$ on the same side of the ring as O5$^\prime$.Figure 7 shows the formulae of the bases, the types of sugar pucker and the numbering of the polynucleotide. Z-DNA is formed at higher salt concentrations for polynucleotides with alternating purine-pyrimidine sequences, i.e. (AT)_n or (GC)_n and has the opposite helicity sense to A or B-DNA (i.e. it is a left-handed helix). The Z-DNA helix is long and thin with a very deep minor groove and almost no major groove.

 

Figure 7

Dye molecules, if fairly flat, can intercalate between the bases of DNA and several such structures, using small polynucleotides, have been studied. The phenomenon is well-illustrated by rotating a spring or `slinky'.

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