Z-DNA
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2008-06-21T22:38:43Z
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[[Image:Z-DNA orbit animated small.gif|right|frame|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-DNA|A-]] and B-DNA.
==History==
Z-DNA was the first single-crystal X-ray structure of a DNA fragment (a self-complementary DNA hexamer d(CG)<sub>3</sub>). It was resovled 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 [[Massachusetts Institute of Technology|MIT]].<ref name=Wang1979>{{cite journal |author=Wang AHJ, Quigley GJ, Kolpak FJ, Crawford JL, van Boom JH, Van der Marel G, Rich A |title=Molecular structure of a left-handed double helical DNA fragment at atomic resolution |journal=Nature (London) |volume=282 |pages=680–686 |year=1979 |doi=10.1038/282680a0}} PMID 514347</ref> The crystallisation of a B- to Z-DNA junction in 2005<ref name=Ha2005>{{cite journal |author=Ha SC, Lowenhaupt K, Rich A, Kim YG, Kim KK |title=Crystal structure of a junction between B-DNA and Z-DNA reveals two extruded bases |journal=Nature |volume=437 |pages=1183–1186 |year=2005 |doi=10.1038/nature04088 |pmid=16237447}}</ref> 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.<ref name="Placido2007">{{cite journal |title=A left-handed RNA double helix bound by the Zalpha domain of the RNA-editing enzyme ADAR1 |author=Placido D, Brown BA 2nd, Lowenhaupt K, Rich A, Athanasiadis A |journal=Structure |volume=15 |issue=4 |pages=395–404 |year=2007 |pmid=17437712 |doi=10.1016/j.str.2007.03.001}}</ref>
==Structure==
[[Image:B-, Z-DNA junction 2ACJ.png|right|thumb|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 poly(dGC)<sub>2</sub>), [[DNA supercoil]]ing or low salt and some [[cation]]s (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.<ref name="ZhangH2006">{{cite journal |author=Zhang H, Yu H, Ren J, Qu X |title=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 |journal=Biophysical Journal |volume=90 |pages=3203–3207 |year=2006 |doi=10.1529/biophysj.105.078402 |url=http://www.biophysj.org/cgi/content/full/90/9/3203 |pmid=16473901}}</ref>
===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).<ref name=Champ2004>{{cite journal |author=Champ PC, Maurice S, Vargason JM, Camp T, Ho PS |title=Distributions of Z-DNA and nuclear factor I in human chromosome 22: a model for coupled transcriptional regulation |journal=Nucleic Acids Res. |volume=32 |issue=22 |pages=6501–10 |year=2004 |pmid=15598822 |doi=10.1093/nar/gkh988 |url=http://nar.oxfordjournals.org/cgi/pmidlookup?view=long&pmid=15598822}}</ref>
Z-Hunt is available at [http://gac-web.cgrb.oregonstate.edu/zDNA/ 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 ([[DNA supercoiling|supercoiling]]) while DNA transcription occurs.<ref name=Rich2003>{{cite journal |author=Rich A, Zhang S |title=Timeline: Z-DNA: the long road to biological function |journal=Nature Rev Genet |volume=4 |pages=566–572 |year=2003 |doi=10.1038/nrg1115}}</ref><ref name=Ha2005>{{cite journal |author=Ha SC, Lowenhaupt K, Rich A, Kim YG, Kim KK |title=Crystal structure of a junction between B-DNA and Z-DNA reveals two extruded bases |journal=Nature |volume=437 |pages=1183–1186 |year=2005 |doi=10.1038/nature04088}}</ref> The potential to form a Z-DNA structure also correlates with regions of active [[transcription (biology)|transcription]]. A comparison of regions with a high sequence-dependent, predicted propensity to form Z-DNA in [[Chromosome 22 (human)|human chromosome 22]] with a selected set of known gene [[Transcription (genetics)|transcription sites]] suggests there is a correlation.<ref name=Champ2004>{{cite journal |author=Champ PC, Maurice S, Vargason JM, Camp T, Ho PS |title=Distributions of Z-DNA and nuclear factor I in human chromosome 22: a model for coupled transcriptional regulation |journal=[[Nucleic Acids Research]] |volume=32 |issue=22 |pages=6501–6510 |year=2004 |doi=10.1093/nar/gkh988 |pmid=15598822}}</ref>
Z-DNA formed after transcription initiation in some cases may be bound by RNA modifying enzymes which then alter the sequence of the newly-formed RNA [http://web.mit.edu/newsoffice/1999/zdna-0911.html].
==Comparison Geometries of Some DNA Forms==
[[Image:A-DNA, B-DNA and Z-DNA.png|right|thumb|Side view of A-, B-, and Z-DNA.]]
[[Image:B&Z&A DNA formula.jpg|thumb|right|250px|The helix axis of A-, B-, and Z-DNA.]]
{| class="wikitable"
|-
!Geometry attribute
!A-form
!B-form
!Z-form
|-
|Helix sense ||align="center"| right-handed ||align="center"| right-handed ||align="center"| left-handed
|-
|Repeating unit ||align="right"| 1 bp ||align="right"| 1 bp ||align="right"| 2 bp
|-
|Rotation/bp ||align="right"| 32.7° ||align="right"| 35.9° ||align="right"| 60°/2
|-
|bp/turn ||align="right"| 11 ||align="right"| 10.5 ||align="right"| 12
|-
|Inclination of bp to axis ||align="right"| +19° ||align="right"| −1.2° ||align="right"| −9°
|-
|Rise/bp along axis ||align="right"| 2.3 Å (0.23 nm)||align="right"| 3.32 Å (0.332 nm)||align="right"| 3.8 Å (0.38 nm)
|-
|Pitch/turn of helix ||align="right"| 28.2 Å (2.82 nm)||align="right"| 33.2 Å (3.32 nm)||align="right"| 45.6 Å (4.56 nm)
|-
|Mean propeller twist ||align="right"| +18° ||align="right"| +16° ||align="right"| 0°
|-
|Glycosyl angle ||align="center"| anti ||align="center"| anti ||align="center"| C: anti,<br> G: syn
|-
|Sugar pucker ||align="center"| C3'-endo ||align="center"| C2'-endo ||align="center"| C: C2'-endo,<br>G: C2'-exo
|-
|Diameter ||align="right"| 23 Å (2.3 nm)||align="right"| 20 Å (2.0 nm)||align="right"| 18 Å (1.8 nm)
|}
==References==
{{reflist}}
===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==
* [http://gac-web.cgrb.oregonstate.edu/zDNA/ ZHunt Online Server]
{{Nucleic acids}}
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