Figure 2.

The Mms4–Mus81 complex is a structure-specific endonuclease. A variety of ³²P-labeled model substrates were incubated with increasing amounts of Mms4–Mus81 and the products were resolved on a native polyacrylamide gel prior to autoradiography. (A) Unbranched substrates. (Lanes 1–5) A 49-nucleotide single-stranded DNA (oligonucleotide 892*); (lanes 6–10) double-stranded DNA (892*/897). (B) Branched substrates. (Lanes 1–5) A Y-shaped substrate (892*/895); (lanes 6–10) a Holliday junction (892*/893/894/895). (C) Cleavage specificity. (Lanes 1–7) A Y-shaped substrate (892/895*), in which oligo 895 is 3′ end labeled; (lanes 8–14) the same substrate in which oligo 892 is 5′ end labeled. Titrations illustrated by a triangle represent 0, 2, 4, 8, and 20 ng of Mms4–Mus81. (*) The presence of a ³²P-phosphate label at the 5′ position unless indicated otherwise. (Δ) The reaction mixture was boiled prior to loading.