Sandbox Z-DNA: Difference between revisions

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== Structure ==
== Structure ==
<applet load='2acj' size='280' frame='true' align='left' caption=' B-Z DNA ' scene ='Sandbox_Z-DNA/B-z/7' />
<applet load='2acj' size='280' frame='true' align='left' caption=' B-Z DNA ' scene ='Sandbox_Z-DNA/B-z/7' />
Z-DNA <scene name='Sandbox_Z-DNA/B-z/7'>(default scene)</scene> 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 moving  RNA polymerase when it moves through 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'>(default scene)</scene> 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 moving  RNA polymerase when it moves through 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>
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== Comparison of the three helices and helical parameters of DNA ==
== Comparison of the three helices and helical parameters of DNA ==
<applet load='A-DNA.pdb' size='300' frame='true' align='right' caption='' />
''Sources''<ref>PMID: 19417072</ref>
<applet load='B-DNA.pdb' size='300' frame='true' align='right' caption='Insert caption here' />
 
<applet load='Z-DNA.pdb' size='300' frame='true' align='right' caption='Insert caption here' />
<applet load='A-DNA_ali.pdb' size='350' frame='true' align='right' caption='A-DNA' align='left' scene ='Sandbox_Z-DNA/A-dna_ali/1'/>
<applet load='B-DNA_ali.pdb' size='350' frame='true' align='right' caption='B-DNA' align='left' scene ='Sandbox_Z-DNA/B-dna_ali/1'/>
<applet load='Z-DNA_ali.pdb' size='350' frame='true' align='right' caption='Z-DNA' align='left' scene ='Sandbox_Z-DNA/Z-dna_ali/1'/>
<jmol>
<jmol>
   <jmolRadioGroup>
   <jmolRadioGroup>
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       <script>sync* OFF</script>
       <script>sync* OFF</script>
       <text>Unsynchronize </text>
       <text>Unsynchronize </text>
    </item>
  </item>
 
   </jmolRadioGroup>
   </jmolRadioGroup>
</jmol>
</jmol>


''Sources''<ref>PMID: 19417072</ref>
{| class="wikitable" align= "center''
 
{| class="wikitable"
|-
|-
!Parameter
!Parameter
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|Residues per turn ||align="right"| 11 ||align="right"| 10.5 ||align="right"| 12
|Residues per turn ||align="right"| 11 ||align="right"| 10.5 ||align="right"| 12
|-
|-
|Axial rise(A°) ||align="right"| 2.55 ||align="right"| 3.4 ||align="right"| 3.7
|Axial rise [Å] ||align="right"| 2.55 ||align="right"| 3.4 ||align="right"| 3.7
|-
|-
|Helix pitch(°) ||align="right"| 28 ||align="right"| 34 ||align="right"| 45
|Helix pitch(°) ||align="right"| 28 ||align="right"| 34 ||align="right"| 45
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|Rotation per residue (°) ||align="right"| 33||align="right"| 36||align="right"|-30
|Rotation per residue (°) ||align="right"| 33||align="right"| 36||align="right"|-30
|-
|-
|Diameter of helix (A°) ||align="right"| 23||align="right"| 20||align="right"| 18
|Diameter of helix [Å]||align="right"| 23||align="right"| 20||align="right"| 18
|-
|-
|Glycosidic bond configuration<br\>dA,dT,dC<br\>dG ||align="center"| <br\>anti<br\>anti ||align="center"| <br\>anti<br\>anti ||align="center"| <br\>anti<br\>syn
|Glycosidic bond configuration<br\>dA,dT,dC<br\>dG ||align="center"| <br\>anti<br\>anti ||align="center"| <br\>anti<br\>anti ||align="center"| <br\>anti<br\>syn
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|Sugar pucker<br\>dA,dT,dC<br\>dG ||align="center"| <br\>C3'-endo<br\>C3'-endo ||align="center"|<br\> C2'-endo<br\>C2'-endo ||align="center"| <br\>C2'-endo<br\>C3'-endo
|Sugar pucker<br\>dA,dT,dC<br\>dG ||align="center"| <br\>C3'-endo<br\>C3'-endo ||align="center"|<br\> C2'-endo<br\>C2'-endo ||align="center"| <br\>C2'-endo<br\>C3'-endo
|-
|-
|Intrastrand phosphate-phosphate distance (A°)<br\>dA,dT,dC<br\>dG ||align="center"| <br\>5.9<br\>5.9||align="center"| <br\>7.0<br\>7.0||align="center"| <br\>7.0<br\> 5.9
|Intrastrand phosphate-phosphate distance [Å] <br\>dA,dT,dC<br\>dG ||align="center"| <br\>5.9<br\>5.9||align="center"| <br\>7.0<br\>7.0||align="center"| <br\>7.0<br\> 5.9
|-
|-
|colspan="4"|''Sources:<ref name="Rich1984">PMID:6383204</ref><ref name="Rich1979">PMID: 514347</ref><ref> Sinden, Richard R (1994-01-15). ''DNA structure and function'' (1st ed.). Academic Press. pp. 398. ISBN 0-12-645750-6.</ref>
|colspan="4"|''Sources:<ref name="Rich1984">PMID:6383204</ref><ref name="Rich1979">PMID: 514347</ref><ref> Sinden, Richard R (1994-01-15). ''DNA structure and function'' (1st ed.). Academic Press. pp. 398. ISBN 0-12-645750-6.</ref>
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