KINEMAGE 1:
B-DNA; Section 3-2B; Figure 3-9.
KINEMAGE 2: The Watson-Crick Base Pairs; Figure 3-11
Derived from the kinemage exercise on the Voet, Voet, and Pratt CD-ROM.
DNA, the archive of hereditary information, forms double helices whose component strands are complementary and antiparallel. In this exercise, we explore the structure of the Watson-Crick double helix, B-DNA (Fig. 3-9). We then study the structures of the Watson-Crick base pairs (Fig. 3-11).
KINEMAGE 1: B-DNA (Section 3-2B; Fig. 3-9).
View1 shows B-DNA with its helix axis vertical and looking down its 2-fold axis of symmetry into its minor groove. All atoms of the 12-bp duplex helix are shown as large balls (with C, N, O, and P atoms white, blue, red, and seagreen) that, for the sake of clarity, are slightly smaller than space-filling size.
Use the "Backbone" and "Bases" buttons under the "Spacefilling" button to turn the base pairs and the two sugar-phosphate chains of the duplex on and off separately. Use the "MinorGroove" and "MajorGroove" buttons to highlight the minor and major grooves (in cyan and yellow). Turning on the "MinorGroove" button highlights, in cyan, an atom that lines the minor groove on each base (atoms C2, O2, N2, and O2 on A, T, G, and C, respectively). Turning on the "MajorGroove" button highlights, in yellow, an atom that lines the major groove on each base (atoms N6, O4, O6, and N4 of A, T, G, and C, respectively)
Views2 through 4 are different orientations of the DNA.
Compare View1 (similar to Fig. 3-9) and View2 of B-DNA. Note that its major
groove is considerably wider than its minor groove although the two grooves
are more or less equally deep. This is particularly evident in View3, a view
along the grooves in which the major groove faces left in the center of the
DNA and the minor grooves faces left near both the top and bottom of the DNA.
The different widths of the grooves arise from the asymmetry of the ribose-phosphate
groups that comprise their walls.
In View1 or View2, turn off the "Backbone" button under the "Spacefilling" button, to see that the base pairs form a solid stack in which the bases are in van der Waals contact (the apparent gaps between the bases are due to the less-than-van der Waals radii of the balls representing the atoms). Turn off the "Spacefilling" button and turn on the upper "SingleStrnd" button to display the path taken by one of the two identical polynucleotide strands of the B-DNA. Note that even the bases in a single strand of B-DNA are well stacked. Now turn off both the "Spacefilling" and upper "SingleStrnd" buttons and then turn on the "Wireframe" button to display the entire duplex molecule in stick form colored skyblue with its ribose ring oxygen atoms represented by small red balls. The backbone and bases can be individually controlled with the corresponding "Backbone" and "Bases" buttons . The "Top bp" button highlights the top base pair in white. Turn on the lower (below the dashed line) "SingleStrand" button to highlight one of the sugar-phosphate backbone strands in magenta. Turn on the associated "Bases" button to highlight the bases of this strand in gold. Turn off the "Wireframe" button to trace the pathway of a single strand of B-DNA. Then, turn on the upper "SingleStrnd" button, so the B-DNA is displayed with one of its strands in skeletal form and the other in spacefilling form.