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Forms of DNA
From Proteopedia
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<target>AtoB</target> | <target>AtoB</target> | ||
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| - | <script> moveto 1.0 0 0 1 0 180.0 0.0 0.0;restore state ab | + | <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> |
<text>Shift in Base Pair between A-B DNA</text> | <text>Shift in Base Pair between A-B DNA</text> | ||
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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 | + | <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> |
<text>Change in Sugar Puckering from C2' endo in B-DNA to C3' endo in A-DNA</text> | <text>Change in Sugar Puckering from C2' endo in B-DNA to C3' endo in A-DNA</text> | ||
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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 | + | <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> |
<text>Transition between A-B DNA spacefilling models</text> | <text>Transition between A-B DNA spacefilling models</text> | ||
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<text>Shift in Base Pair between A-B DNA</text> | <text>Shift in Base Pair between A-B DNA</text> | ||
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| - | <script> moveto 1.0 0 0 1 0 400.0 0.0 0.0; restore state ab;cartoon OFF | + | <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> |
<text>Change in Sugar Puckering from C2' endo in B-DNA to C3' endo in A-DNA</text> | <text>Change in Sugar Puckering from C2' endo in B-DNA to C3' endo in A-DNA</text> | ||
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<text>Transition between A-B DNA spacefilling models</text> | <text>Transition between A-B DNA spacefilling models</text> | ||
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Revision as of 11:33, 5 February 2018
See DNA - History of the discovery and current applications (Hebrew)
Contents |
A comparative representation of the three forms of DNA
Sources[1]
| A-DNA | B-DNA | Z-DNA | ||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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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
| Drag the structure with the mouse to rotate |
References
- ↑ http://203.129.231.23/indira/nacc/
- ↑ 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
- ↑ 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
- ↑ Sinden, Richard R (1994-01-15). DNA structure and function (1st ed.). Academic Press. pp. 398. ISBN 0-12-645750-6.
- ↑ 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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Angel Herraez, Jaime Prilusky, Michal Harel, Adithya Sagar, Eran Hodis, Karsten Theis, Eric Martz
