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 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).