B-DNA tour: Difference between revisions
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==B-form DNA== | ==B-form DNA== | ||
<StructureSection load='1bna' size='400' side='right' caption='B-DNA' scene='72/725442/B-dna_overview/2'> | <StructureSection load='1bna' size='400' side='right' caption='B-DNA [[1bna]]' scene='72/725442/B-dna_overview/2'> | ||
Source <ref>PMID:7071593</ref> | |||
== Structural highlights == | == Structural highlights == | ||
<UL> | <UL> | ||
<LI> Most common DNA conformation in vivo | <LI> Most common DNA conformation ''in vivo'' | ||
<LI> Narrower, more elongated helix than A | <LI> Narrower, more elongated helix than A-form | ||
<LI> Wide major groove easily accessible to proteins | <LI> Wide major groove easily accessible to proteins | ||
<LI> Narrow minor groove | <LI> Narrow minor groove | ||
<LI> Favored conformation at high water concentrations (hydration of minor groove seems to favor B-form) | <LI> Favored conformation at high water concentrations (hydration of minor groove seems to favor B-form) | ||
<LI> Base pairs nearly perpendicular to helix axis | <LI> Base pairs nearly perpendicular to helix axis | ||
<LI> Sugar pucker C2'-endo | <LI> Sugar pucker C2'-''endo'' | ||
</UL> | </UL> | ||
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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 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. | ||
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'> | 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'>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='72/725442/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. | ||
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. | 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 [http://proteopedia.org/wiki/images/d/d3/JnABZ3d.gif 3D red-blue | You can compare it with the DNA forms by looking at this [http://proteopedia.org/wiki/images/d/d3/JnABZ3d.gif 3D red-blue stereo picture of A, B, and Z DNA] | ||
</StructureSection> | </StructureSection> | ||
==See Also== | |||
* [[Z-DNA model tour]] and [[Z-DNA]] | |||
* [[A-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 == | ||
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 /> | |||
Latest revision as of 00:36, 26 January 2021
B-form DNAB-form DNA
Source [1] Structural highlights
Take the TourThe tour starts with the view. Now look at this .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. Now change the display to make it show the 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. You can .You are looking into the major groove and the colors of the base pairs alternate. You can also . Each base pair stacks on the next similarly, as shown from . This is the . A-form DNA also stacks in this way, but compare this with Z-DNA, which behaves much differently. 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 . 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 3D red-blue stereo picture of A, B, and Z DNA |
| ||||||||||
See AlsoSee Also
- Z-DNA model tour and Z-DNA
- A-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 DNA Structure, disponible también en español and eight other languages.
ReferencesReferences
JSmol in Proteopedia [2] or to the article describing Jmol [3] to the rescue.
- ↑ 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
- ↑ 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
- ↑ 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