FIG. 1.
(A) The 5′ (right-end) hairpin of MVM displayed as a simple duplex stem structure in the flip configuration. A small internal palindrome positioned near the top of the stem potentially allows this region to reconfigure into the asymmetric cruciform structure shown in panel B. At its most extended position, the four-way junction at the core of this cruciform is 85 bp from the nick site. As detailed in panel C, the internal palindrome contains two 10-mer [(ACCA)2.5] sequence repeats, boxed with solid lines, which constitute NS1 binding sites positioned in opposite orientations around the twofold symmetry axis. Additional tetranucleotide motifs which likely contribute to NS1 binding are boxed with dashed lines. In panels A and B, the shaded boxes represent binding sites which position NS1 over the nick site. (D) Autoradiograph of a nondenaturing polyacrylamide gel showing a 32P-, 3′-end-labeled hairpin origin before (lane 1) and after (lane 2) cleavage with MspI. Following incubation with NS1 and HMG1 in the presence of ATP, the hairpin substrate is nicked and covalently associated with NS1 (lane 3), while the substrate precut with MspI remains unmodified (lane 4).