Z-DNA model tour: Difference between revisions

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Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

James Nolan, Michal Harel

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 Now change the display to make it show the <scene name='72/725870/Space_filling_bbone/1'>sugar-phosphate backbone as pseudo-bonds</scene>  connecting the phosphate atoms.  Now the bases are easier to see.  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. But notice that the base pairs do not stack upon each other equivalently. The backbone also is not a continuous curve, it "zig-zags" back and forth (hence "Z"-DNA).
-<scene name='72/725870/Zoom_pair/1'>In this view</scene>, the molecule is shown in stick representation, with the backbone in yellow and sets of base pairs in red and blue. Notice how the blue bases stack well on the adjacent blue ones, but not on adjacent red ones, and vice versa. So it is the dinucleotide unit, rather than mononucleotide that is the repeating unit of the structure.  This explains the need for alternating purines and pyrimidines to form Z-DNA.
+<scene name='72/725870/Zoom_pair/2'>In this view</scene>, the molecule is shown in stick representation, with the backbone in yellow and sets of base pairs in red and blue. Notice how the blue bases stack well on the adjacent blue ones, but not on adjacent red ones, and vice versa. So it is the dinucleotide unit, rather than mononucleotide that is the repeating unit of the structure.  This explains the need for alternating purines and pyrimidines to form Z-DNA.
-You can see <scene name='72/725870/Zoom_pairs_only/1'>the same view without the backbone</scene> here.Going 5' to 3', there is good stacking within the GpC dinucleotide, but not between them (CpG).
+You can see <scene name='72/725870/Zoom_pairs_only/2'>the same view without the backbone</scene> here.Going 5' to 3', there is good stacking within the GpC dinucleotide, but not between them (CpG).
 A <scene name='72/725870/Zoom_pair_top/1'>top view</scene> also illustrates the stacking arrangement. You can also see this <scene name='72/725870/Zoom_pairs_only_top/1'>top view of just the bases.</scene>. Note the stacking of red base pairs on each other is much different than the stacking of red on blue.