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[1].
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)[2]. 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[3]. Whenever Z-DNA forms, there must be two junction boxes that allow the flip back to the canonical B-form of DNA.
Contents
Abstracts
Biologists were puzzled by the discovery of left-handed Z-DNA because it seemed unnecessary. Z-DNA was stabilized by the negative supercoiling generated by transcription, which indicated a transient localized conformational change. Few laboratories worked on the biology of Z-DNA. However, the discovery that certain classes of proteins bound to Z-DNA with high affinity and great specificity indicated a biological role. The most recent data show that some of these proteins participate in the pathology of poxviruses.[4]
Forty-nine years ago Watson and Crick proposed a double-stranded (ds-) model for DNA. This double helix has become an icon of molecular biology. Twenty-six years later, Rich accidently discovered Z-DNA, an exotic left-handed nucleic acid. For many years thereafter, this left-handed DNA was thought to be an artifact. DNA is no longer looked upon as a static molecule but rather an extremely dynamic structure in which different conformations are in equilibrium with each other. Many researchers have spent the last two decades characterizing this novel left-handed DNA structure. Now many investigators are beginning to accept the possibility that this novel ds-DNA conformation may play a significant in vivo role within eukaryotic and prokaryotic cells. However, more research needs to be performed before it is absolutely accepted by all in the scientific community.[5]
Left-handed Z-DNA is a higher-energy form of the double helix, stabilized by negative supercoiling generated by transcription or unwrapping nucleosomes. Regions near the transcription start site frequently contain sequence motifs favourable for forming Z-DNA, and formation of Z-DNA near the promoter region stimulates transcription. Z-DNA is also stabilized by specific protein binding; several proteins have been identified with low nanomolar binding constants. Z-DNA occurs in a dynamic state, forming as a result of physiological processes then relaxing to the right-handed B-DNA. Each time a DNA segment turns into Z-DNA, two B-Z junctions form. These have been examined extensively, but their structure was unknown. Here we describe the structure of a B-Z junction as revealed by X-ray crystallography at 2.6 A resolution. A 15-base-pair segment of DNA is stabilized at one end in the Z conformation by Z-DNA binding proteins, while the other end remains B-DNA. Continuous stacking of bases between B-DNA and Z-DNA segments is found, with the breaking of one base pair at the junction and extrusion of the bases on each side (Fig. 1). These extruded bases may be sites for DNA modification.[3]
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
- Citations
- ↑ 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
- ↑ 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
- ↑ 3.0 3.1 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
- ↑ Rich A, Zhang S (2003). Timeline: Z-DNA: the long road to biological function. Nat Rev Genet, 4(7):566-72.
- ↑ Gagna CE, Lambert WC (2003). The halting arrival of left-handed Z-DNA. Med Hypotheses, 60(3):418-23.
- General references
- 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.
- 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.
- Eichman BF, Schroth GP, Basham BE, and Ho PS (1999). The intrinsic structure and stability of out-of-alternation base pairs in Z-DNA. Nucleic Acids Res, 27(2):543-550.
- Ho PS (1994). The non-B-DNA structure of d(CA/TG)n does not differ from that of Z-DNA. Proc Natl Acad Sci USA, 91(20):9549-9553.
- Sniden RR (1994). DNA structure and function. Academic Press, 179-216.
- Kagawa TF, Howell ML, Tseng K, and Ho PS (1993). Effects of base substituents on the hydration of B- and Z-DNA: correlations to the B- to Z-DNA transition. Nucleic Acids Res, 21(25):5978-5986.
- Ellison MJ, Fenton MJ, Ho PS, and Rich A (1987). Long-range interactions of multiple DNA structural transitions within a common topological domain. EMBO J, 6(5):1513-1522.
- Ho PS, Ellison MJ, Quigley GJ, and Rich A (1986). A computer aided thermodynamic approach for predicting the formation of Z-DNA in naturally occurring sequences. EMBO J, 5(10):2737-2744.
- Kelleher RJ 3rd, Ellison MJ, Ho PS, and Rich A (1986). Competitive behavior of multiple, discrete B-Z transitions in supercoiled DNA. Proc Natl Acad Sci USA, 83(17):6342-6346.
- Ho PS, Frederick CA, Quigley GJ, van der Marel GA, van Boom JH, Wang AH, and Rich A (1985). G.T wobble base-pairing in Z-DNA at 1.0 A atomic resolution: the crystal structure of d(CGCGTG). EMBO J, 4(13A):3617-3623.
- 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.
