B-DNA tour: Difference between revisions
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==B-form DNA== | ==B-form DNA== | ||
<StructureSection load='1bna' size='340' side='right' caption='B-DNA' scene='72/725442/B-dna_overview/1'''> | <StructureSection load='1bna' size='340' side='right' caption='B-DNA' scene='72/725442/B-dna_overview/1'''> | ||
== Structural highlights == | |||
<UL> | <UL> | ||
<LI> Most common DNA conformation in vivo | <LI> Most common DNA conformation in vivo | ||
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</UL> | </UL> | ||
== | == Take the Tour == | ||
Start the tour with this <scene name='72/725442/B-dna_overview/1'>Overview</scene> view. Now look at this <scene name='72/725442/Space_filling_view/1'>space filling view</scene>.The backbone is yellow and the bases are magenta. | Start the tour with this <scene name='72/725442/B-dna_overview/1'>Overview</scene> view. Now look at this <scene name='72/725442/Space_filling_view/1'>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. | ||
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 <scene name='72/725442/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 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/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 and are nearly perpendicular to the axis of the double helix. Note also that the backbone forms a smooth, continuous curve. | ||
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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 | 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> | ||
== References == | == References == | ||
R. E. Dickerson, H. R. Drew, B. N. Conner, R. M. Wing, A. V. Fratini & M. | 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> | 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. | |||
Revision as of 01:20, 21 February 2016
B-form DNAB-form DNA
Structural highlights
Take the TourStart the tour with this 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. Each base pair stacks on the next similarly, as shown from . 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 stern picture of A, B, and Z DNA |
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ReferencesReferences
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 [1] JSmol in Proteopedia [2] or to the article describing Jmol [3] to the rescue.