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Figure 3.
Base flipping outside of the recognition sequence. (A) Superimposition of the
two DNA duplexes, bound with molecule A (colored in grey) or molecule B (colored with
yellow for carbon atoms, blue for nitrogen atoms, red for oxygen atoms and magenta for
phosphate atoms). Base pairs are numbered from 1 to 10, as shown in Figure 2A. The
distances between the stacked bases on strand F are indicated. For comparison, the flipped
Ade, A(3) of strand E, and its corresponding A(3) of strand C are enlarged and boxed. (B)
The flipped Ade, A(3) of strand E, lies against the HinP1I protein surface of molecule B.
The double arrows indicate van der Waals contacts. (C) A view of DNA structure containing
a junction between Z-DNA and B-DNA [PDB 2ACJ ([213]17)]. The two bases of a A:T base pair
at the junction are extruded. Note the van der Waals interaction (double arrow) between
the extruded Thy and an intrahelical base.
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