FIG. 1.

Structure of the right-hand hairpin. (A) The 5′ (right) hairpin of MVM displayed as a simple duplex stem structure, in the flip configuration. Flip comprises 121 potential bp, with three unpaired thymidine residues forming the turnaround at the top of the stem. Twenty base pairs in from this end, three unpaired residues, AGA, form a small asymmetric bubble. This region of the stem harbors a small internal palindrome centered on the three-nucleotide (n) mismatch, and thus an alternative structure in which the duplex assumes an asymmetric cruciform configuration is possible. This cruciform is created by the concertina-like rearrangement of the palindrome, so that its size and position on the stem can vary slightly. At its most extended position (B), the four-way junction at its core is 85 bp from the nick site. Two nucleotides which would be unpaired in the cruciform structure are also indicated. The flop sequence is simply the inverted complement of flip. The cross-hatched box indicates the sequence 5′-AACCAACTGAACCA-3′, which forms the binding site for an NS1 molecule whose footprint would project over the nick site.