FIGURE 3.

The secondary structure of a DTJ arrangement. A DTJ is composed of three consecutive double helices, H1, H2, and H3. In all known DTJs the central helix H2 contains either 2 or 3 bp. At both ends, H2 is flanked by helices H1 and H3, which, to be qualified as such, should contain at least one WC or GU base pair. At the junction points between the helices, there are two over-twists, which occur in the opposite strands. One over-twist (TJ1) has a higher amplitude than the other one (TJ2); this difference is used here for alignment of different DTJs.