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Figure 1.
Fig. 1. Structure of the stacked-X DNA Holliday junction.
The structure of d(CCGGTACCGG) (ACC-J) as a four-stranded
junction (11) is shown with the inside cross-over strands
colored in yellow and green and the outside noncrossing strands
in blue and red. The pairs of stacked duplex arms are
highlighted with cylinders. Details of the molecular
interactions that stabilize junctions are in crystals are shown,
with the essential H-bond from the C[8] cytosine to the
phosphate of the cross-over C[7] nucleotide in the blue box, and
the weaker H-bond from C7 to A6 in the ACC-J or the weak
electrostatic interaction from the methyl of T7 to A6 in
d(CCGATATCGG) (ATC-J) in the red boxes (12, 16).
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