International
Tables for
Crystallography
Volume F
Crystallography of biological macromolecules
Edited by M. G. Rossmann and E. Arnold

International Tables for Crystallography (2006). Vol. F. ch. 23.3, pp. 600-601   | 1 | 2 |

Section 23.3.3.6. Biological applications of A, B and Z helices

R. E. Dickersona*

aMolecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095–1570, USA
Correspondence e-mail: red@mbi.ucla.edu

23.3.3.6. Biological applications of A, B and Z helices

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The B helix is the biologically relevant structure for DNA. The A form might logically be adopted at the stage of transient DNA–RNA duplexes during transcription, but elsewhere the B form holds sway. It was once thought that binding of DNA to a protein surface, most particularly nucleosomal winding, might constitute a sufficient dehydration of bound water molecules from the DNA duplex to shift it to the A form. This proved to be false; nucleosomal DNA clearly retains the B conformation. The closest that one comes to biological A-DNA is local deformations upon binding of B-DNA to a few proteins that have been described as `A-like distortions'. On the other hand, the A helix has been found repeatedly in RNA duplexes, including tRNA and ribozymes.

The situation is even more restrictive with the Z helix. Although its alternating purine/pyrimidine sequence makes it unusable for genetic coding, the suggestion has been made on many occasions that Z-DNA might be an important element in genetic control by being involved in negative supercoiling (Herbert & Rich, 1996[link]). It has been shown that a left-handed DNA conformation can be induced by negative superhelical stress, but it is not absolutely clear that this induced, left-handed conformation is the same as the Z helix seen in crystal structures of small oligomers. As noted by Herbert & Rich (1996)[link], after nearly twenty years of enquiry, it is still far from certain that Z-DNA itself has any demonstrable biological role.1

A major stumbling block is the cumbersome mechanism that must be invoked to explain a B-to-Z interconversion. As mentioned previously, a simple twisting of the helix from right to left is not sufficient, because the backbone chains run in opposite directions in the two forms. Fig. 23.3.3.6[link] demonstrates the steps that must still be undertaken after both B and Z helices have been unwound so as to remove all of their helical character. Note the opposite sense of the backbone strands in B [part (a)] and Z [part (e)]. In order to accomplish the interconversion, base pairs of B-DNA must be pulled apart, as in part (b), and each base pair swung around to the opposite side of the backbone `ladder' [part (c)]. This would automatically lead to syn conformations at both ends of the base pair, as drawn in Fig. 23.3.3.4(b)[link]. Returning pyrimidines to an anti conformation would create the zigzag backbone chain (Fig. 23.3.3.4c)[link]. Base pairs can then be re-stacked, as in parts (d) and (e) in Fig. 23.3.3.6[link] (which differ only by rotation of the entire helix about the vertical), to yield the backbone geometry of a Z helix. This is the simplest interconversion and one which was recognized and proposed in the very first Z-DNA structure paper (Z1). Other alternatives have been suggested, involving breaking individual base pairs, swinging the bases independently around their backbone chains, and re-forming the pairs. But one kind of special mechanism or another must be invoked if a B-to-Z interconversion is to be achieved.

[Figure 23.3.3.6]

Figure 23.3.3.6 | top | pdf |

Interconversion of a B to a Z helix. Because the strands have opposite directions in B (a) and Z (e), interconversion must involve opening up the helix (b), flipping each base pair to the other side (c), and re-stacking base pairs (d). (d) and (e) are identical upon rotation about a vertical axis.

References

First citationHerbert, A. & Rich, A. (1996). The biology of left-handed Z-DNA. J. Biol. Chem. 271, 11595–11598.Google Scholar








































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