KINEMAGE 1:
B-DNA; Section 3-2B; Figure 3-9.
KINEMAGE 2: The Watson-Crick Base Pairs; Figure 3-11
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.
KINEMAGE 2: The Watson-Crick Base Pairs (Section 3-2A; Fig. 3-11).
View1 shows an A-T Watson-Crick base pair from ideal B-DNA (Fig. 3-11). The C, N, and O atoms of the bases (including ribose atom C1(, the glycosidic carbon atom) are represented by gray, blue, and red balls, respectively, that can be turned on and off with the "Base Atoms" button. The bonds of the thymine (T) base are yellow and those of the adenine (A) base are seagreen. The 5(-ribose phosphate groups, which can be turned on and off with the "Ribose Phos." button, are magenta and their ribose ring oxygen atoms are represented by small red balls. The hydrogen bonds through which the bases are paired are represented by dashed white lines that can be turned on and off with the "H bonds" button.
Click the "ANIMATE" button to replace the A-T base pair with a G-C Watson-Crick base pair. The G-C pair is colored identically to the A-T pair except that the bonds of the guanine (G) base are skyblue and those of the cytosine (C) base are orange. Note that the atomic positions of the ribose phosphate groups, including those of the glycosidic carbons, are unchanged by this base pair switch.
View2 shows the bases edgewise. There would likewise be no change in the atomic positions of the ribose phosphate groups if the A-T and G-C base pairs were replaced by T-A or C-G. Thus, the conformation of a DNA's sugar-phosphate backbone is unaffected by the identities of its Watson-Crick base pairs. This is one of the requirements for building a regular helix whose structure is independent of sequence. View2 also shows that the two ribose-phosphate groups in each base pair are oriented oppositely, making the DNA's sugar-phosphate backbones antiparallel. The bases in DNA lie at smaller distances from the helix axis than the sugar phosphate backbones, so each DNA double helix has two helical grooves running along its periphery (we examined these grooves in KINEMAGE 1).
Identify the atoms of each base-pair that point toward the major and minor grooves. These grooves can be easily identified as follows: Go back to View1 and turn on the "Glycosid.Bon" button to highlight the glycosidic bonds in red. The minor groove is the one in which the two glycosidic bonds of the base pair make an angle of less than 180 degrees. The groups that line the minor groove are donated by the edges of the bases that face the opening of this angle. Turn on the "MinorGroove" button to highlight, 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). Click on the center of an atom to cause its atom type to appear in the lower left corner of the screen. Similarly, the edges of the bases that face the opening of the angle made by the glycosidic bonds that is greater than 180 degrees line the DNA's so-called major groove. Turn on the "MajorGroove" button to highlight, 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).