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20-September-2008 09:29:10 - Z-DNA The Z-DNA structure. The Z-DNA structure. 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 1 History 2 Structure 2.1 Predicting Z-DNA structure 3 Biological significance 4 Comparison Geometries of Some DNA Forms 5 References 5.1 Further reading 6 See also 7 External links History Z-DNA was the first single-crystal X-ray structure of a DNA fragment a self-complementary DNA hexamer dCG3. It was resolved as a left-handed double helix with two anti-parallel chains that were held together by Watson-Crick base pairs see: x-ray crystallography. It was solved by Andrew Wang, Alexander Rich, and co-workers in 1979 at MIT.1 The crystallisation of a B- to Z-DNA junction in 20052 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. In 2007, the RNA version of Z-DNA, Z-RNA, was described as a transformed version of an A-RNA double helix into a left-handed helix.3 Structure B-/Z-DNA junction bound to a Z-DNA binding domain. Note the two highlighted extruded bases. From PDB 2ACJ. B-/Z-DNA junction bound to a Z-DNA binding domain. Note the two highlighted extruded bases. From PDB 2ACJ. 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 especially polydGC2, negative DNA supercoiling or low salt and some cations all at physiological temperature, 37°C, and pH 7.3-7.4. Z-DNA can form a junction with B-DNA in a structure which involves the extrusion of a base pair. The Z-DNA conformation has been difficult to study because it does not exist as a stable feature of the double helix. Instead, it is a transient structure that is occasionally induced by biological activity and then quickly disappears.4 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.5 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.62 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.5 Z-DNA formed after transcription initiation in some cases may be bound by RNA modifying enzymes, such as ADAR1, which then alter the sequence of the newly-formed RNA 1. Comparison Geometries of Some DNA Forms Side view of A-, B-, and Z-DNA. Side view of A-, B-, and Z-DNA. The helix axis of A-, B-, and Z-DNA. The helix axis of A-, B-, and Z-DNA. 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 32.7° 35.9° 60°/2 bp/turn 11 10.5 12 Inclination of bp to axis +19° -1.2° -9° Rise/bp along axis 2.3 Ã… 0.23 nm 3.32 Ã… 0.332 nm 3.8 Ã… 0.38 nm Pitch/turn of helix 28.2 Ã… 2.82 nm 33.2 Ã… 3.32 nm 45.6 Ã… 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 23 Ã… 2.3 nm 20 Ã… 2.0 nm 18 Ã… 1.8 nm References ^ Wang AHJ, Quigley GJ, Kolpak FJ, Crawford JL, van Boom JH, Van der Marel G, Rich A 1979. Molecular structure of a left-handed double helical DNA fragment at atomic resolution. Nature London 282: 680-686. doi:10.1038/282680a0. PMID 514347 ^ a b Ha SC, Lowenhaupt K, Rich A, Kim YG, Kim KK 2005. Crystal structure of a junction between B-DNA and Z-DNA reveals two extruded bases. Nature 437: 1183-1186. doi:10.1038/nature04088. PMID 16237447. ^ Placido D, Brown BA 2nd, Lowenhaupt K, Rich A, Athanasiadis A 2007. A left-handed RNA double helix bound by the Zalpha domain of the RNA-ing enzyme ADAR1. Structure 15 4: 395-404. doi:10.1016/j.str.2007.03.001. PMID 17437712. ^ Zhang H, Yu H, Ren J, Qu X 2006. Reversible B/Z-DNA Transition under the Low Salt Condition and Non-B-Form PolydApolydT Selectivity by a Cubane-Like Europium-L-Aspartic Acid Complex. Biophysical Journal 90: 3203-3207. doi:10.1529/biophysj.105.078402. PMID 16473901. ^ a b Champ PC, Maurice S, Vargason JM, Camp T, Ho PS 2004. Distributions of Z-DNA and nuclear factor I in human chromosome 22: a model for coupled transcriptional regulation. Nucleic Acids Res. 32 22: 6501-10. doi:10.1093/nar/gkh988. PMID 15598822. ^ Rich A, Zhang S 2003. Timeline: Z-DNA: the long road to biological function. Nature Rev Genet 4: 566-572. doi:10.1038/nrg1115. 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 v d e Types of nucleic acids Constituents Nucleobases | Nucleosides | Nucleotides | Deoxynucleotides Ribonucleic acids RNA | mRNA pre-mRNA/hnRNA | tRNA | rRNA | aRNA | gRNA | miRNA | ncRNA | piRNA | shRNA | siRNA | snRNA | snoRNA | stRNA | ta-siRNA | tmRNA Deoxyribonucleic acids DNA | cDNA | gDNA | msDNA | mtDNA Nucleic acid analogues GNA | LNA | PNA | TNA | morpholino Cloning vectors phagemid | plasmid | lambda phage | cosmid | P1 phage | fosmid | BAC | YAC | HAC Major families of biochemicals Saccharides | Carbohydrates | Glycosides | | Amino acids | Peptides | Proteins | Glycoproteins | | Lipids | Terpenes | Steroids | Carotenoids Alkaloids | Nucleobases | Nucleic acids | | Enzyme cofactors | Flavonoids | Polyketides | Tetrapyrroles Retrieved from http://en..org/wiki/Z-DNA Categories: DNA Views Article Discussion this page History Personal tools Log in / create account Navigation Main page Contents Featured content Current events Random article Search Go Search Interaction Community portal Recent changes Contact Donate to Help Toolbox What links here Related changes Upload file Special pages Printable version Permanent link Cite this page Languages ÄŒesky Deutsch Türkçe УкраїнÑ?ька ä¸æ–‡ This page was last modified on 8 August 2008, at 02:07
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