This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


Forms of DNA

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
(improve synchromization)
(buttons for other renderings)
Line 28: Line 28:
{{Clear}}
{{Clear}}
 +
 +
Change rendering:
 +
<jmol>
 +
<jmolButton>
 +
<target>AtoB</target> <!--this is on purpose to the other applet, otherwise "script applet" skips the current one -->
 +
<script>script applet "A,B,Z" @{"define temp selected; set cartoonRibose on; select all;cartoon -0.01;color cartoon indianRed;select polymer=2;color cartoon darkOrchid;select _P;cpk 35%;select temp;"};</script>
 +
<text>cartoons</text>
 +
</jmolButton>
 +
<jmolButton>
 +
<target>AtoB</target>
 +
<script>script applet "A,B,Z" @{"define temp selected;select all;spacefill only;select temp;"};</script>
 +
<text>spacefilling for all</text>
 +
</jmolButton>
 +
<jmolButton>
 +
<target>AtoB</target>
 +
<script>script applet "A,B,Z" @{"define temp selected;select all;wireframe -0.3;select temp;"};</script>
 +
<text>sticks (initial display)</text>
 +
</jmolButton>
 +
</jmol>
 +
 +
=== Helical Parameters of the three forms of DNA ===
=== Helical Parameters of the three forms of DNA ===

Revision as of 11:08, 5 February 2018

See DNA - History of the discovery and current applications (Hebrew)

See Also: DNA and Z-DNA

Contents

A comparative representation of the three forms of DNA

Sources[1]

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

Drag the structure with the mouse to rotate


Morph Sources [5] / Morphs


References

  1. ↑ http://203.129.231.23/indira/nacc/
  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
Retrieved from "http://52.214.119.220/wiki/index.php/Forms_of_DNA"
Personal tools