Z-DNA
Z-DNA is a 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 (Wang et al. 1979).
Z-DNA is quite different from the right-handed forms. Z-DNA is often compared against B-DNA in order to illustrate the major differences. This unique type of DNA can form alternating purine-pyrimidine tracts under very specific conditions. These conditions include high salt, the presence of some cations, and DNA supercoiling.
An algorithm for predicting the propensity of DNA to flip from the B-form to the Z-form, Z-Hunt, was written by Dr. P. Shing Ho in 1984. 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) (Champ et al. 2004). Z-Hunt is available at Z-Hunt online.
After 26 years of attempts, Rich et al. finally crystalised the junction box of B- and Z-DNA. Their results were published in an October 2005 Nature journal (Ha et al. 2005). Whenever Z-DNA forms, there must be two junction boxes that allow the flip back to the canonical B-form of DNA.
Contents
Representation of various forms of DNA
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 | 2.3Å | 3.32Å | 3.8Å |
| Pitch/turn of helix | 24.6Å | 33.2Å | 45.6Å |
| 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 | 26Å | 20Å | 18Å |
References
- 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.
- 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.
- Sniden RR (1994). DNA structure and function. Academic Press 179-216.
- 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.
