Z-DNA: Difference between revisions

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<StructureSection load='Z-DNA.pdb' size='400' side='right' scene='Z-DNA/Z-dna_new/1' caption=''>
<StructureSection load='Z-DNA.pdb' size='350' side='right' scene='Z-DNA/Z-dna_new/1' caption=''>


'''Z-DNA''' <scene name='Z-DNA/Z-dna_new/1'>(default scene)</scene> is  a form of DNA that has a different structure from the more common <scene name='Sandbox_Z-DNA/Bdna/3'>B-DNA</scene> form.It is a left-handed double helix wherein the sugar-phosphate backbone has a zigzag pattern due to the alternate stacking of bases in [http://proteopedia.org/wiki/index.php/Syn_and_anti_nucleosides anti-conformation and syn conformation]. In Z-DNA only a minor groove is present and the major groove is absent. The residues that allow sequence-specific recognition of Z-DNA are present on the convex outer surface.<ref name = 'Rich'> PMID:12838348</ref>  This DNA form is thought to play a role in the regulation of gene expression, DNA processing events and/or genetic instability.<ref name = 'Wang'>PMID:17485386</ref>
'''Z-DNA''' <scene name='Z-DNA/Z-dna_new/1'>(default scene)</scene> is  a form of DNA that has a different structure from the more common <scene name='Sandbox_Z-DNA/Bdna/3'>B-DNA</scene> form.It is a left-handed double helix wherein the sugar-phosphate backbone has a zigzag pattern due to the alternate stacking of bases in [http://proteopedia.org/wiki/index.php/Syn_and_anti_nucleosides anti-conformation and syn conformation]. In Z-DNA only a minor groove is present and the major groove is absent. The residues that allow sequence-specific recognition of Z-DNA are present on the convex outer surface.<ref name = 'Rich'> PMID:12838348</ref>  This DNA form is thought to play a role in the regulation of gene expression, DNA processing events and/or genetic instability.<ref name = 'Wang'>PMID:17485386</ref>
See also [[Z-DNA model tour]] and [[B-DNA tour]].


== Structure ==
== Structure ==


Z-DNA (<scene name='Sandbox_Z-DNA/B-z/7'>B-Z DNA junction</scene>, PDB entry [[2acj]]) can form ''invitro'' from B-DNA by raising negative super helical stress or under low salt conditions when deoxycytosine is 5-methylated. The formation of Z-DNA ''invivo'' is an energy requiring process. It forms behind a RNA polymerase moving through a DNA double helix during transcription and is subsequently stabilized due to the generation of negative supercoils. Z-DNA is the first single crystal X-ray structure of a DNA fragment. It was crystallized as a self complementary DNA hexamer d(CG)<sub>3</sub> by Andrew Wang, Alexander Rich and their co-workers at MIT in 1979. <ref name = 'Rich'>PMID:12838348</ref><ref name ='Wang'>PMID:17485386</ref>
Z-DNA (<scene name='Sandbox_Z-DNA/B-z/7'>B-Z DNA junction</scene>, PDB entry [[2acj]]) can form ''in vitro'' from B-DNA by raising negative super helical stress or under low salt conditions when deoxycytosine is 5-methylated. The formation of Z-DNA ''in vivo'' is an energy requiring process. It forms behind a RNA polymerase moving through a DNA double helix during transcription and is subsequently stabilized due to the generation of negative supercoils. Z-DNA is the first single crystal X-ray structure of a DNA fragment. It was crystallized as a self complementary DNA hexamer d(CG)<sub>3</sub> by Andrew Wang, Alexander Rich and their co-workers at MIT in 1979. <ref name = 'Rich'>PMID:12838348</ref><ref name ='Wang'>PMID:17485386</ref>


Whenever B-DNA transforms into Z-DNA two <scene name='Sandbox_Z-DNA/B-zjunction/7'>B-Z junctions</scene> form. The crystal structure of these junctions revealed<scene name='Sandbox_Z-DNA/Extruded/12'> two extruded bases</scene>, <scene name='Z-DNA/Extruded/2'>adenine</scene>  and <scene name='Z-DNA/Extruded/3'>thymine</scene> at the junction. A crucial finding from this structure is that a right handed DNA can transform to a left handed DNA or vice versa by the disruption and extrusion of a base pair. It has also been suggested that the extruded base pairs at B-Z DNA junction may be sites for DNA modification.<ref>PMID:16237447</ref>
Whenever B-DNA transforms into Z-DNA two <scene name='Sandbox_Z-DNA/B-zjunction/7'>B-Z junctions</scene> form. The crystal structure of these junctions revealed<scene name='Sandbox_Z-DNA/Extruded/12'> two extruded bases</scene>, <scene name='Z-DNA/Extruded/2'>adenine</scene>  and <scene name='Z-DNA/Extruded/3'>thymine</scene> at the junction. A crucial finding from this structure is that a right handed DNA can transform to a left handed DNA or vice versa by the disruption and extrusion of a base pair. It has also been suggested that the extruded base pairs at B-Z DNA junction may be sites for DNA modification.<ref>PMID:16237447</ref>
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__NOTOC__
__NOTOC__
== Movie Depicting ADAR1 binding to Z-DNA ==
== Movie Depicting ADAR1 binding to Z-DNA ==
<qt>file=Movie3_Z-DNA.mov|width=320|height=280|autoplay=false|controller=true</qt>
<html5media height="315" width="560">http://www.youtube.com/embed/tvrWkld8TBY</html5media>
 
== Comparison of the three helices and helical parameters of DNA ==
== Comparison of the three helices and helical parameters of DNA ==
''Sources''<ref>http://203.129.231.23/indira/nacc/</ref>
''Sources''<ref>http://203.129.231.23/indira/nacc/</ref>
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Updated on {{REVISIONDAY2}}-{{MONTHNAME|{{REVISIONMONTH}}}}-{{REVISIONYEAR}}
Updated on {{REVISIONDAY2}}-{{MONTHNAME|{{REVISIONMONTH}}}}-{{REVISIONYEAR}}


[[1woe]], [[3qba]] – ZDNA hexamer CGCGCG<br />
[[1woe]], [[3qba]], [[1i0t]], [[6aqt]], [[6aqv]], [[6aqw]], [[6aqx]], [[2ie1]], [[1da1]], [[1ick]], [[313d]], [[314d]], [[390d]], [[391d]], [[392d]], [[3p4j]], [[3qba]], [[3wbo]], [[400d]], [[4fs5]], [[4fs6]], [[4hif]], [[4hig]], [[2hto]], [[2htt]], [[4r15]], [[4xsn]], [[6bst]] – ZDNA hexamer CGCGCG<br />
[[1v9g]] – ZDNA hexamer CGCGCG - Neutron<br />
[[1tne]] – ZDNA hexamer CGCGCG - NMR<br />
[[2obz]] – ZDNA hexamer CGCGUG<br />
[[362d]] – ZDNA hexamer TGCGCA<br />
[[1qbj]] – ZDNA hexamer CGCGCG + hADAR1 Zα domain - human<br />
[[1qbj]] – ZDNA hexamer CGCGCG + hADAR1 Zα domain - human<br />
[[2heo]] - ZDNA hexamer CGCGCG + Z-DNA-binding protein Zα domain – mouse<br />
[[2heo]] - ZDNA hexamer CGCGCG + Z-DNA-binding protein Zα domain – mouse<br />
[[2eyi]] - ZDNA hexamer CGCGCG + Z-DNA-binding protein Zβ domain<br />
[[1sfu]] - ZDNA hexamer CGCGCG + Pox virus Z-DNA-binding protein Zα domain <br />
[[4wcg]] - ZDNA hexamer CGCGCG + Herpes virus 3 Z-DNA-binding protein Zα domain <br />
[[1j75]] - ZDNA hexamer CGCGCG + DLM-1 Z-DNA-binding protein Zα domain <br />
[[3f21]] - ZDNA hexamer CACGTG + double-stranded RNA-specific adenosine deaminase Z-DNA-binding protein Zα domain <br />
[[3f21]] - ZDNA hexamer CGTACG + double-stranded RNA-specific adenosine deaminase Z-DNA-binding protein Zα domain <br />
[[3eyi]] - ZDNA hexamer CGCGCG + Z-DNA-binding protein Zβ domain<br />
[[1j75]] - ZDNA hexamer CGCGCG + DLM-1 Zα domain<br />
[[1j75]] - ZDNA hexamer CGCGCG + DLM-1 Zα domain<br />
[[3fqb]] - ZDNA hexamer CGCGTG + Ba<br />


==Additional Resources==
==Additional Resources==
Retrieved from "https://proteopedia.org/Z-DNA"