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Forms of DNA

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(alternative to display A to B transition (the previous tags are not woring now))
Current revision (17:42, 24 August 2023) (edit) (undo)
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See DNA - History of the discovery and current applications (Hebrew)
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== A comparative representation of the three forms of DNA ==
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''See Also: [[DNA]] and [[Z-DNA]]''
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=== A comparative representation of the three forms of DNA ===
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''Sources'' <ref>Nucleic Acid Canonical Coordinates http://nucleix.mbu.iisc.ac.in/nacc/index.html</ref>
''Sources'' <ref>Nucleic Acid Canonical Coordinates http://nucleix.mbu.iisc.ac.in/nacc/index.html</ref>
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</jmol>
</jmol>
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=== Helical Parameters of the three forms of DNA ===
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== Helical Parameters of the three forms of DNA ==
DNA is a very flexible molecule and has the ability to exist in various forms based on the environmental conditions. Naturally occurring DNA double helices are classified into A, B and Z-types. A and B-forms of DNA are the right handed forms whereas [[Z-DNA]] is the left handed form. When hydrated the DNA generally assumes B-form. The A conformation is found when there is little water to interact with the helix and is also the conformation adopted by the RNA. The formation of Z-DNA occurs with the methylation of deoxycytosine residues and also during transcription where negative supercoiling stabilizes it.
DNA is a very flexible molecule and has the ability to exist in various forms based on the environmental conditions. Naturally occurring DNA double helices are classified into A, B and Z-types. A and B-forms of DNA are the right handed forms whereas [[Z-DNA]] is the left handed form. When hydrated the DNA generally assumes B-form. The A conformation is found when there is little water to interact with the helix and is also the conformation adopted by the RNA. The formation of Z-DNA occurs with the methylation of deoxycytosine residues and also during transcription where negative supercoiling stabilizes it.
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|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
|-
|-
-
|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
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|[[Sugar ring pucker|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 [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
|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
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<!-- Generation of smooth transition between animated morphs each of which depicts a different change-->
<!-- Generation of smooth transition between animated morphs each of which depicts a different change-->
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<StructureSection load='' size='350' side='right' caption='Transition between A and B forms of DNA double helix' scene='43/438459/Sticks/1'>
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<!-- Loading and animating Initial Morph-->
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This animated model displays the structural transformation between A and B forms of DNA
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<StructureSection load='' name='AtoB' size='550' side='left' caption='Transition between A and B forms of DNA double helix' scene='43/438459/Spacefill_animated/3'>
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</StructureSection>
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This animated model displays the structural transformation between A and B forms of DNA.
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Rendering: <jmol>
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<jmolButton>
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<target>AtoB</target>
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<script>wireframe -0.2;</script>
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<text>Sticks</text>
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</jmolButton>
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<jmolButton>
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<target>AtoB</target>
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<script>spacefill only; save state ab;</script>
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<text>Spacefill</text>
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</jmolButton>
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</jmol> <scene name='43/438459/Spacefill_animated/3'>Reset the model</scene>
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<!-- Loading and animating Initial Morph-->
 
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<jmol>
 
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<jmolApplet>
 
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<name>AtoB</name>
 
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<size>660</size>
 
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<color>white</color>
 
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<uploadedFileContents>morph_a-b.pdb</uploadedFileContents>
 
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<script>animation ON; animation mode PALINDROME; cartoon ON; save state ab </script> <!-- State is saved here when page loads but unable to restore state. It is being required to save state again and then restore works-->
 
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</jmolApplet>
 
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</jmol>
 
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<!--To activate the below options saving initial state again as restore state after above step is not working-->
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Control of animation:<jmol>
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<jmol>
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<jmolRadioGroup>
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<jmolButton>
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<target>AtoB</target>
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<target>AtoB</target>
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<vertical>true</vertical>
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<script>moveto 1.0 0 0 1 0 100.0 0.0 0.0;load/wiki/images/9/9e/Morph_a-b.pdb;animation ON; animation mode PALINDROME; cartoon ON;save state ab</script> <!-- This is required as the initial save state is unable to restore state-->
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<text>Click here and activate the below options </text>
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</jmolButton>
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</jmol>
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<!--Group of Actions which show base pair shift, sugar pucker change and difference in space filling models in A and B DNA -->
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<jmol>
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<jmolRadioGroup>
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<target>AtoB</target>
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<item>
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<script> moveto 1.0 0 0 1 0 180.0 0.0 0.0;restore state ab; animation mode palindrome;animation ON;cartoon ON;spacefill on; spacefill 90;wireframe on;wireframe 50;zoom 180;select 9:a,4:b;hbonds ON;hbonds calculate;hbonds 0.09;select not selected; color translucent 0.9;set echo bottom centre;font echo 20 serif bolditalic;color echo green; echo "Base pair shift between A and B DNA"</script>
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<text>Shift in Base Pair between A-B DNA</text>
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</item>
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<item>
<item>
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<script> moveto 1.0 0 0 1 0 400.0 0.0 0.0; restore state ab;cartoon OFF;spacefill ON; spacefill 90; wireframe ON; wireframe 50;select 9:a; select not selected; color translucent 0.9; select not selected; centre selected;zoom 400;set echo bottom centre;font echo 20 serif bolditalic;color echo green; echo "Change in Sugar Puckering from C2' endo in B-DNA to C3' endo in A-DNA"; animation mode palindrome;animation ON;</script>
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<script>frame pause; frame last;</script>
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<text>Change in Sugar Puckering from C2' endo in B-DNA to C3' endo in A-DNA</text>
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<text>A-DNA (without conformational animation)</text>
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</item>
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</item>
<item>
<item>
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<script>moveto 1.0 0 0 1 0 150.0 0.0 0.0;restore state ab;spacefill ON; spacefill 400; zoom 150; cartoon OFF; animation mode PALINDROME;animation ON; set echo bottom centre;font echo 20 serif bolditalic;color echo green; echo"Transition between A-B DNA spacefilling models"; </script>
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<script>frame pause; frame rewind;</script>
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<text>Transition between A-B DNA spacefilling models</text>
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<text>B-DNA (without conformational animation)</text>
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</item>
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</item>
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</jmolRadioGroup>
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<item>
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<script>frame play;</script>
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<text>restore animated conformational change</text>
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<checked>true</checked>
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</item>
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</jmolRadioGroup>
</jmol>
</jmol>
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<!-- Restores Original State for Applet 4-->
 
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<jmol>
 
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<jmolButton>
 
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<target>AtoB</target>
 
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<script>moveto 1.0 0 0 1 0 100.0 0.0 0.0;load/wiki/images/9/9e/Morph_a-b.pdb;animation ON; animation mode PALINDROME; cartoon ON;save state ab</script>
 
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<text>Restore Original State </text>
 
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</jmolButton>
 
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</jmol>
 
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<!--Group of actions which show base pair shift, sugar pucker change and difference in space filling models in A and B DNA -->
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<!-- Applet 5-->
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Other interesting views:<jmol>
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<!--<jmol>
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<jmolRadioGroup>
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<jmolApplet>
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<target>AtoB</target>
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<color>white</color>
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<vertical>true</vertical>
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<size>660</size>
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<uploadedFileContents>Morph_test.pdb</uploadedFileContents>
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<script>animation ON;animation mode PALINDROME;cartoon ON; save state ab_new</script>
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</jmolApplet>
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</jmol>
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<jmol>
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<jmolButton>
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<target>6</target>
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<script>moveto 1.0 0 0 1 0 100.0 0.0 0.0;load/wiki/images/5/50/Morph_test.pdb;animation ON; animation mode PALINDROME; cartoon ON;save state ab</script>
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<text>Click here and activate options below </text>
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</jmolButton>
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</jmol>
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<jmol>
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<jmolRadioGroup>
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<target>6</target>
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<item>
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<script> moveto 1.0 0 0 1 0 180.0 0.0 0.0;restore state ab;define temp selected; cartoon ON; spacefill 90; wireframe 50;zoom 180;select 9:a,4:b;hbonds calculate;hbonds 0.09; color translucent 0.9;set echo bottom centre;font echo 20 serif bold;color echo green; echo"Shift in Base Pair between A-B DNA"; select temp; animation mode palindrome;animation ON; </script>
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<text>Shift in Base Pair between A-B DNA</text>
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</item>
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<item>
<item>
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<script> moveto 1.0 0 0 1 0 400.0 0.0 0.0; restore state ab;define temp selected; cartoon OFF; spacefill 90; wireframe 50;select not 9:a; color translucent 0.9; centre selected;zoom 400;set echo bottom centre;font echo 20 serif bold;color echo green; echo"Change in Sugar Puckering from C2' endo in B-DNA to C3' endo in A-DNA"; select temp; refresh; animation mode palindrome;animation ON; </script>
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<script>spin off; select all; cartoon only; spacefill 90; wireframe 50; centre all; zoom 180;
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<text>Change in Sugar Puckering from C2' endo in B-DNA to C3' endo in A-DNA</text>
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color translucent 0.9; select 9:A,4:B; hbonds calculate; hbonds 0.09; color opaque;
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</item>
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set echo bottom centre; font echo 18 serif bold; color echo green; echo "Base pair shift between A and B DNA";
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moveto 1 0 0 1 0 180 0 0;</script>
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<text>Shift in base pair between A- and B- DNA</text>
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</item>
<item>
<item>
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<script>moveto 1.0 0 0 1 0 150.0 0.0 0.0;restore state ab;define temp selected; cartoon OFF;spacefill 400; zoom 150; set echo bottom centre;font echo 20 serif bold;color echo green; echo"Transition between A-B DNA spacefilling models"; select temp; animation mode palindrome;animation ON; </script>
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<script>spin off; select all; spacefill only; spacefill 90; wireframe 50;
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<text>Transition between A-B DNA spacefilling models</text>
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color translucent 0.9; select 9:A; color opaque; centre selected; zoom 400;
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</item>
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set echo bottom left; font echo 18 serif bold; color echo green; echo "Change in sugar puckering |from C2' endo in B-DNA to C3' endo in A-DNA";
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</jmolRadioGroup>
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moveto 1 0 0 1 0 400 0 0;</script>
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<text>Change in sugar puckering from C2' endo in B-DNA to C3' endo in A-DNA</text>
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</item>
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<item>
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<script>set echo bottom centre; echo;
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centre all; moveto 1 {688 565 -455 102.5} 100 0 0; select all; spacefill only; spin on;
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color opaque;</script>
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<text>Original display (spacefill)</text>
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</item>
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</jmolRadioGroup>
</jmol>
</jmol>
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<jmol>
 
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<jmolButton>
 
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<target>6</target>
 
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<script>moveto 1.0 0 0 1 0 100.0 0.0 0.0;load/wiki/images/5/50/Morph_test.pdb;animation ON; animation mode PALINDROME; cartoon ON;save state ab</script>
 
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<text>Restore Original State </text>
 
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</jmolButton>
 
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</jmol>-->
 
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''Morph Sources'' <ref>PMID: 10734184</ref> / [[Morphs]]
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Source of morphs: <ref>PMID: 10734184</ref>
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[[Morphs|Read more about morphing]]
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</jmol>-->
</jmol>-->
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== References==
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</StructureSection>
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== See also ==
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* [[DNA - History of the discovery and current applications (Hebrew)]]
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* [[DNA]]
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* [[Z-DNA]]
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 +
== References ==
<references/>
<references/>

Current revision

Contents

A comparative representation of the three forms of DNA

Sources [1]

To re-align the three molecules, reload this page.
A-DNA B-DNA Z-DNA
Drag the structure with the mouse to rotate
Drag the structure with the mouse to rotate
Drag the structure with the mouse to rotate

Change rendering:

Helical Parameters of the three forms of DNA

DNA is a very flexible molecule and has the ability to exist in various forms based on the environmental conditions. Naturally occurring DNA double helices are classified into A, B and Z-types. A and B-forms of DNA are the right handed forms whereas Z-DNA is the left handed form. When hydrated the DNA generally assumes B-form. The A conformation is found when there is little water to interact with the helix and is also the conformation adopted by the RNA. The formation of Z-DNA occurs with the methylation of deoxycytosine residues and also during transcription where negative supercoiling stabilizes it.

Parameter A-DNA B-DNA Z-DNA
Helix sense right-handed right-handed left-handed
Residues per turn 11 10.5 12
Axial rise [Å] 2.55 3.4 3.7
Helix pitch(°) 28 34 45
Base pair tilt(°) 20 −6 7
Rotation per residue (°) 33 36-30
Diameter of helix [Å] 23 20 18
Glycosidic bond configuration
dA,dT,dC
dG
anti
anti
anti
anti
anti
syn
Sugar pucker
dA,dT,dC
dG
C3'-endo
C3'-endo
C2'-endo
C2'-endo
C2'-endo
C3'-endo
Intrastrand phosphate-phosphate distance [Å]
dA,dT,dC
dG
5.9
5.9
7.0
7.0
7.0
5.9
Sources: [2][3][4]

Structural Transformation between A and B DNA

Transition between A and B forms of DNA double helix

Drag the structure with the mouse to rotate

See also

References

  1. ↑ Nucleic Acid Canonical Coordinates http://nucleix.mbu.iisc.ac.in/nacc/index.html
  2. ↑ Rich A, Nordheim A, Wang AH. The chemistry and biology of left-handed Z-DNA. Annu Rev Biochem. 1984;53:791-846. PMID:6383204 doi:http://dx.doi.org/10.1146/annurev.bi.53.070184.004043
  3. ↑ Wang AH, Quigley GJ, Kolpak FJ, Crawford JL, van Boom JH, van der Marel G, Rich A. Molecular structure of a left-handed double helical DNA fragment at atomic resolution. Nature. 1979 Dec 13;282(5740):680-6. PMID:514347
  4. ↑ Sinden, Richard R (1994-01-15). DNA structure and function (1st ed.). Academic Press. pp. 398. ISBN 0-12-645750-6.
  5. ↑ Krebs WG, Gerstein M. The morph server: a standardized system for analyzing and visualizing macromolecular motions in a database framework. Nucleic Acids Res. 2000 Apr 15;28(8):1665-75. PMID:10734184
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