Figure 2.

Substrate preferences of the Slx1–4 nuclease. Under standard assay conditions, 4 fmole of the indicated 5′-[³²P]-labeled substrate was incubated with 0, 10, 20, 30, or 40 fmole of Slx1–4. The reactions were terminated, and the products were resolved by native 10% PAGE in 1× TBE. (A) Unbranched substrates were assembled from the following oligonucleotides: ssDNA (lanes 1–5), *891; dsDNA (lanes 6–10), *888/896; nicked DNA (lanes 11–15), *891/994/1084; 3′ extension (lanes 16–20), *891/994; and 5′ extension (lanes 16–20), *891/1084. (B) Branched substrates were assembled from the following oligonucleotides: Y (lanes 1–5), 888/*891; 5′ flap (lanes 6–10), 888/*891/992; 3′ flap (lanes 11–15), 888/*891/994; replication fork (lanes 16–20), 888/*891/992/994; fixed HJ (4wF, lanes 21–25), 888/889/890/*891; and mobile HJ (4wM, lanes 26–30), *892/893/894/895. (C) The quantity of undigested substrate remaining in the reactions shown in B was determined and is presented as a function of Slx1–4 concentration. The positions of reaction products are indicated on the left of A and B. An asterisk represents the 5′-[³²P] label.