Z-DNA
From Wikipedia, the free encyclopedia
Z-DNA is a left-handed helical form of DNA 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 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[1].
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. This unique type of DNA forms under sequence-dependent conditions that require an alternating purine-pyrimidine sequence. Other chemical environmental factors favor the formation of Z-DNA such as high salt, the presence of some cations, and DNA supercoiling.
While no definitive biological significance of Z-DNA has been found, it is commonly believed to provide torsional strain relief while DNA transcription occurs.[2][3]
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)[4]. Z-Hunt is available at Z-Hunt online. 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[4].
After 26 years of attempts, Rich et al. finally crystallized the junction box of B- and Z-DNA. Their results were published in an October 2005 Nature journal[3]. Whenever Z-DNA forms, there must be two junction boxes that allow the flip back to the canonical B-form of DNA.
Contents |
[edit] Representation of various forms of DNA
[edit] 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) |
[edit] References
- ^ Wang AHJ, Quigley GJ, Kolpak FJ, Crawford JL, van Boom JH, Van der Marel G, and Rich A (1979). Molecular structure of a left-handed double helical DNA fragment at atomic resolution. Nature (London), 282:680-686.
- ^ Rich A, Zhang S (2003). Timeline: Z-DNA: the long road to biological function. Nature Rev Genet, 4:566–572.
- ^ a b Ha SC, Lowenhaupt K, Rich A, Kim YG, and Kim KK (2005). Crystal structure of a junction between B-DNA and Z-DNA reveals two extruded bases. Nature, 437:1183-1186.
- ^ a b Champ PC, Maurice S, Vargason JM, Camp T, and Ho PS (2004). Distributions of Z-DNA and nuclear factor I in human chromosome 22: a model for coupled transcriptional regulation. Nucleic Acids Research, 32(22):6501-6510.
[edit] Further reading
- Sinden RR (1994). DNA structure and function. Academic Press, 179-216. ISBN 0-12-645750-6
