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.


A-RNA tour

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (21:07, 11 January 2017) (edit) (undo)
 
(10 intermediate revisions not shown.)
Line 1: Line 1:
==A-form RNA==
==A-form RNA==
-
<StructureSection load='1rna' size='400' side='right' caption='A-RNA' scene='72/725869/A-rna_overview/1'>
+
<StructureSection load='1rna' size='350' side='right' caption='A-RNA [[1rna]]' scene='72/725869/A-rna_overview/1'>
-
<scene name='72/725869/A-rna_overview/1'>TextToBeDisplayed</scene>
+
Source <ref>PMID:7071593</ref>
== Structural highlights ==
== Structural highlights ==
<UL>
<UL>
Line 15: Line 15:
== Take the Tour ==
== Take the Tour ==
-
The tour starts with the <scene name='72/725869/A-rna_overview/1'>Default</scene> view. Now look at this <scene name='72/725442/Space_filling_view/2'>space filling view</scene>.The backbone is yellow and the bases are magenta. Note that the major groove (in the middle, when you have just clicked the button) is wide and easily accessible.
+
The tour starts with the <scene name='72/725869/A-rna_overview/1'>Default</scene> view. Now look at this <scene name='72/725869/Rna_space_filling_view/2'>space filling view</scene>.The backbone is yellow and the bases are magenta. Note that the major groove (at the top, when you have just clicked the button) is very deep.
-
Now change the display to make it show the <scene name='72/725442/Space_filling_bbone/2'>sugar-phosphate backbone as pseudo-bonds</scene> connecting the phosphate atoms. Now the bases are easier to see. Notice how they are stacked upon each other and are nearly perpendicular to the axis of the double helix. Note also that the backbone forms a smooth, continuous curve.
+
Now change the display to make the show the <scene name='72/725869/Rna_space_filling_bbone/1'>sugar-phosphate backbone as pseudo-bonds</scene> connecting the phosphate atoms. Now the bases are easier to see. Notice how they are stacked upon each other but not perpendicular to the axis of the double helix. They are also displaced to the side of the axis. The result is a wide, short helix. Note also that the backbone forms a smooth, continuous curve.
-
You can <scene name='72/725442/Zoom_pairs/1'>look at just four of the base pairs.</scene>.You are looking into the major groove and the colors of the base pairs alternate. You can also <scene name='72/725442/Zoom_pairs_only/1'>looks at just the bases</scene>.
+
You can <scene name='72/725869/Zoom_pairs/1'>look at just four of the base pairs.</scene>.You are looking into the major groove and the colors of the base pairs alternate. You can also <scene name='72/725869/Zoom_pairs_only/1'>look at just the bases</scene>.
-
Each base pair stacks on the next similarly, as shown from <scene name='72/725442/Zoom_pairs_top/1'>this top view</scene>. This is the <scene name='72/725442/Zoom_pairs_only_top/1'>same top view of just the bases</scene>. A-form DNA also stacks in this way, but compare this with Z-DNA, which behaves much differently.
+
Each base pair stacks on the next similarly, as shown from <scene name='72/725869/Zoom_pairs_top/1'>this top view</scene>. This is the <scene name='72/725869/Zoom_pairs_only_top/1'>same top view of just the bases</scene>.
 +
B-DNA stacks similarly, but compare this with Z-DNA, which behaves much differently. Essentially all helical RNA is in A form, but DNA can also be found in A form under certain conditions (particularly in RNA-DNA hybrids). The 2'-OH of ribose favors the C3'-''endo'' sugar pucker necessary for A-form geometry. The O2' is easily seen as white spheres in <scene name='72/725869/Rna_space_filling_o2prime/1'>this space fill view</scene>.
-
DNA is usually found in the B form under physiological conditions. The B-form conformation is stabilized by water molecules bound to the minor groove. You can see them as red dots <scene name='72/725442/Water_spine/1'>in this view</scene>. Sometimes kinks are found in the B helix at transcriptional control regions. These kinks can either be intrinsic to the DNA sequence or caused by transcription factor binding.
+
You can compare it with the DNA forms by looking at this [[Media:JnABZ3d.gif|3D red-blue stereo picture of A, B, and Z DNA]]
-
 
+
-
You can compare it with the DNA forms by looking at this [http://proteopedia.org/wiki/images/d/d3/JnABZ3d.gif 3D red-blue stern picture of A, B, and Z DNA]
+
</StructureSection>
</StructureSection>
 +
==See Also==
 +
* [[Z-DNA model tour]] and [[Z-DNA]]
 +
* [[B-DNA tour]]
 +
*[[Transfer RNA tour]]
 +
* A more general overview will be found at [[DNA]].
 +
* [[Forms of DNA]] shows a side-by-side comparison of A, B, and Z forms of DNA.
 +
* An interactive tutorial on [http://dna.molviz.org DNA Structure], ''disponible también en español'' and eight other languages.
== References ==
== References ==
-
R. E. Dickerson, H. R. Drew, B. N. Conner, R. M. Wing, A. V. Fratini & M.
+
 
-
L. Kopka (1982) The anatomy of A-, B-, and Z-DNA. Science 216: 475-485 <ref>PMID:7071593</ref>
+
JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.
JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.
 +
 +
 +
<references />

Current revision

A-form RNA

A-RNA 1rna

Drag the structure with the mouse to rotate

See Also

References

JSmol in Proteopedia [2] or to the article describing Jmol [3] to the rescue.


  1. ↑ Dickerson RE, Drew HR, Conner BN, Wing RM, Fratini AV, Kopka ML. The anatomy of A-, B-, and Z-DNA. Science. 1982 Apr 30;216(4545):475-85. PMID:7071593
  2. ↑ Hanson, R. M., Prilusky, J., Renjian, Z., Nakane, T. and Sussman, J. L. (2013), JSmol and the Next-Generation Web-Based Representation of 3D Molecular Structure as Applied to Proteopedia. Isr. J. Chem., 53:207-216. doi:http://dx.doi.org/10.1002/ijch.201300024
  3. ↑ Herraez A. Biomolecules in the computer: Jmol to the rescue. Biochem Mol Biol Educ. 2006 Jul;34(4):255-61. doi: 10.1002/bmb.2006.494034042644. PMID:21638687 doi:10.1002/bmb.2006.494034042644

Proteopedia Page Contributors and Editors (what is this?)

James Nolan, Michal Harel

Retrieved from "http://52.214.119.220/wiki/index.php/A-RNA_tour"
Personal tools