|
International
Tables for Crystallography Volume F Crystallography of biological macromolecules Edited by M. G. Rossmann and E. Arnold © International Union of Crystallography 2006 |
International Tables for Crystallography (2006). Vol. F. ch. 23.3, p. 609
Section 23.3.5. Summary
a
Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095–1570, USA |
Three families of nucleic acid double helix have been found – A, B and Z – with widely different structures and usages. The A and B helices are right-handed and have no limitations on base sequence. Z is left-handed and effectively limited to alternating purines and pyrimidines, with G and C overwhelmingly favoured. B is the biologically significant helix for DNA and is used in genetic coding. A is the helix of preference for RNA because it can accommodate the C2′-OH group of ribose, which produces steric clash in the B helix. The Z helix has, as yet, no well established biological function. A left-handed DNA configuration can be induced in longer DNA segments by negative supercoiling in solution, but it is not clear that this left-handed configuration is identical to the Z-DNA seen in short crystalline oligomers, because of the reversed orientation of backbone strands in Z-DNA.
B-DNA is an inherently malleable or deformable duplex. Its sugar ring conformations are much more variable than those of A-DNA. The base sequence of B-DNA is expressed directly via hydrogen bonds between bases of a pair, and indirectly via hydrogen-bond donors and acceptors along the floor of the major and minor groove. Sequence is also expressed as a differential deformability of different regions of the duplex. The two most obvious parameters affected by base sequence are minor groove width and helix bendability. Certain sequences of B-DNA are not statically bent, but are more bendable under stress than are other sequences. Bending occurs via roll, usually in the direction that compresses the broad major groove. Pyrimidine-purine or Y-R steps are most conducive to roll bending, and purine-purine steps are least bendable, particularly A-tracts of four or more AT base pairs without the weak T-A step. Natural selection has engineered Y-R steps into a DNA sequence where a sharp roll bend is wanted, and short A-tracts into a sequence where bending is not desired.
References
Ansevin, A. T. & Wang, A. H. (1990). Evidence for a new Z-type left-handed DNA helix. Nucleic Acids Res. 18, 6119–6126.Google Scholar
Dickerson, R. E. (1983). The DNA helix and how it is read. Sci. Am. 249 (December), 94–111.Google Scholar
Dickerson, R. E. (1998a). Sequence-dependent B-DNA conformation in crystals and in protein complexes. In Structure, motion, interaction and expression of biological macromolecules, edited by R. H. Sarma & M. H. Sarma, pp. 17–36. New York: Adenine Press.Google Scholar
Dickerson, R. E. (1998b). Helix structure and molecular recognition by B-DNA. In Oxford handbook of nucleic acid structure, edited by S. Neidle, ch. 7, pp. 145–197. Oxford University Press.Google Scholar
Dickerson, R. E. (1998c). DNA bending: the prevalence of kinkiness and the virtues of normality. Nucleic Acids Res. 26, 1906–1926.Google Scholar
Dickerson, R. E. & Chiu, T. K. (1997). Helix bending as a factor in protein/DNA recognition. Biopolymers Nucleic Acid Sci. 44, 361–403.Google Scholar
El Hassan, M. A. & Calladine, C. R. (1997). Conformational characteristics of DNA: empirical classifications and a hypothesis for the conformational behaviour of dinucleotide steps. Philos. Trans. R. Soc. London A, 355, 43–100.Google Scholar
Levitt, M. & Warshel, A. (1978). Extreme conformational flexibility of the furanose ring in DNA and RNA. J. Am. Chem. Soc. 100, 2607–2613.Google Scholar
Schneider, B., Neidle, S. & Berman, H. M. (1997). Conformations of the sugar–phosphate backbone in helical DNA crystal structures. Biopolymers, 42, 113–124.Google Scholar
Voet, D. & Voet, J. G. (1990). Biochemistry. New York: John Wiley & Sons. Google Scholar
Voet, D. & Voet, J. G. (1995). Biochemistry, 2nd edition. New York: John Wiley & Sons.Google Scholar
