Difference between revisions of "Z-DNA"
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'''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''' 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 [[Massachusetts Institute of Technology|MIT]] | + | 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 [[Massachusetts Institute of Technology|MIT]].<ref name=wang>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</ref> |
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. | 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) | + | 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).<ref name=champ>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</ref> Z-Hunt is available at [http://gac-web.cgrb.oregonstate.edu/zDNA/ 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 | + | 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.<ref name=ha>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</ref> Whenever Z-DNA forms, there must be two junction boxes that allow the flip back to the canonical B-form of DNA. |
==Representation of various forms of DNA== | ==Representation of various forms of DNA== | ||
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|} | |} | ||
| − | ==References== | + | == References == |
| + | ;Citations | ||
| + | <references/> | ||
| + | ;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. | * 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. | * 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. | ||
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* 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. | * 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. | ||
| − | ==External links== | + | == External links == |
* [http://gac-web.cgrb.oregonstate.edu/zDNA/ ZHunt Online Server] | * [http://gac-web.cgrb.oregonstate.edu/zDNA/ ZHunt Online Server] | ||
[[Category:Academic Research]] | [[Category:Academic Research]] | ||
Revision as of 05:48, 15 July 2006
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
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
- ↑ 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
- 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.
