B-DNA

This JSmol based interactive allows you explore the structure of DNA (CGCAAATTTGCG). Turn off and on the various visualization options: ball-and-stick, cartoon, spacefilling, and spin. Also, turn hydrogen bonds off and on. Make sure you rotate the structure around with each option. Make a special point to view the original view (with the double-helix up and down) and down the helix axis. If you ever get lost, click on the "Reset to Original View" button.

View the AT and GC base pairs with the different options as well. Notice that an AT base pair has two hydrogen bonds and a GC base pair has three. Noting this and the fact that A and G are purines and T and C are pyrimidines allows you easily identify which base is which. Notice that even in this view you can tell that the strands are anti-parallel because of the orientation of the sugar and the position of the phosphate.

Notice also the methyl group of T sticking into the major groove. The pattern of methyl groups and hydrogen bonding donors and acceptors facing the major groove allows the sequence to be read by DNA binding proteins without separating the strands.