Z-DNA

'Z-DNA' is one of the many possible double helical structures of DNA. It is a left-handed double helical structure in which the double helix winds to the left in a zig-zag pattern (instead of to the right, like the more common B-DNA form). Z-DNA is thought to be one of three biologically active double helical structures along with A- and B-DNA.

Contents

History

Structure

Predicting Z-DNA structure

Biological significance

Comparison Geometries of Some DNA Forms

References

Further reading

See Also

External links

History

Z-DNA was the first crystal structure of a DNA molecule to be solved (see: x-ray crystallography). It was solved by Alexander Rich and co-workers in 1979 at MIT. Molecular structure of a left-handed double helical DNA fragment at atomic resolution, Wang AHJ, Quigley GJ, Kolpak FJ, Crawford JL, van Boom JH, Van der Marel G, Rich A, , , Nature (London), 1979 PMID 514347 The crystallisation of a B- to Z-DNA junction in 2005 Crystal structure of a junction between B-DNA and Z-DNA reveals two extruded bases, Ha SC, Lowenhaupt K, Rich A, Kim YG, Kim KK, , , Nature, 2005 provided a better understanding of the potential role Z-DNA plays in cells. Whenever a segment of Z-DNA forms, there must be B-Z junctions at its two ends, interfacing it to the B-form of DNA found in the rest of the genome.

Structure

Z-DNA is quite different from the right-handed forms. In fact, Z-DNA is often compared against B-DNA in order to illustrate the major differences. The Z-DNA helix is left handed and has a structure that repeats every 2 base pairs. The major and minor grooves, unlike A- and B-DNA, show little difference in width. Formation of this structure is generally unfavourable, although certain conditions can promote it; such as alternating purine-pyrimidine sequence, DNA supercoiling or high salt and some cations. Z-DNA can form a junction with B-DNA in a structure which involves the extrusion of a base pair.

Predicting Z-DNA structure

It is possible to predict the likelihood of a DNA sequence forming a Z-DNA structure. An algorithm for predicting the propensity of DNA to flip from the B-form to the Z-form, ''ZHunt'', was written by Dr. P. Shing Ho in 1984 (at MIT). This algorithm was later developed by Tracy Camp, P. Christoph Champ, Sandor Maurice, and Jeffrey M. Vargason for genome-wide mapping of Z-DNA (with P. Shing Ho as the principal investigator). Distributions of Z-DNA and nuclear factor I in human chromosome 22: a model for coupled transcriptional regulation, Champ PC, Maurice S, Vargason JM, Camp T, Ho PS, , , Nucleic Acids Research, 2004
Z-Hunt is available at Z-Hunt online.

Biological significance

While no definitive biological significance of Z-DNA has been found, it is commonly believed to provide torsional strain relief (supercoiling) while DNA transcription occurs. Timeline: Z-DNA: the long road to biological function, Rich A, Zhang S, , , Nature Rev Genet, 2003 Crystal structure of a junction between B-DNA and Z-DNA reveals two extruded bases, Ha SC, Lowenhaupt K, Rich A, Kim YG, Kim KK, , , Nature, 2005 The potential to form a Z-DNA structure also correlates with regions of active transcription. A comparison of regions with a high sequence-dependent, predicted propensity to form Z-DNA in human chromosome 22 with a selected set of known gene transcription sites suggests there is a correlation. Distributions of Z-DNA and nuclear factor I in human chromosome 22: a model for coupled transcriptional regulation, Champ PC, Maurice S, Vargason JM, Camp T, Ho PS, , , Nucleic Acids Research, 2004

Comparison Geometries of Some DNA Forms

Geometry attribute	A-form	B-form	Z-form
Helix sense	right-handed	right-handed	left-handed
Repeating unit	1 bp	1 bp	2 bp
Rotation/bp	33.6°	35.9°	60°/2
Mean bp/turn	10.7	10.0	12
Inclination of bp to axis	+19°	−1.2°	−9°
Rise/bp along axis	2.3 Å (0.23 nm)	3.32 Å (0.332 nm)	3.8 Å (0.38 nm)
Pitch/turn of helix	24.6 Å (2.46 nm)	33.2 Å (3.32 nm)	45.6 Å (4.56 nm)
Mean propeller twist	+18°	+16°	0°
Glycosyl angle	anti	anti	C: anti, G: syn
Sugar pucker	C3'-endo	C2'-endo	C: C2'-endo, G: C2'-exo
Diameter	26 Å (2.6 nm)	20 Å (2.0 nm)	18 Å (1.8 nm)

References

Further reading

★ Sinden RR (1994). DNA structure and function. ''Academic Press'', 179-216. ISBN 0-12-645750-6

★ Rich A, Zhang S (2003). Timeline: Z-DNA: the long road to biological function. ''Nat Rev Genet, 4:566–572''.

See Also

★ Mechanical properties of DNA

★ DNA

★ A-DNA

★ B-DNA

External links

★ ZHunt Online Server