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. Author manuscript; available in PMC: 2012 Jul 3.

Published in final edited form as: Biochemistry. 2011 Apr 27;50(20):4360–4370. doi: 10.1021/bi200333k

(A) Metnase preferentially cleaves ssDNA overhang of flap and pseudo Y DNA. Wt-Metnase (0 or 50 ng) was incubated with 100 fmol of 5′-P³²-labeled DNA substrate indicated on the top (see Table 1 for the details of individual substrates) for 60 min prior to 12% denatured PAGE (+ 8M urea) analysis. Lanes “M” represent DNA markers. (B) Metnase exhibits both 3′- and 5′-ssDNA overhang cleavage activity. Metnase (0 or 50 ng) was incubated with 5′-flap DNA (lanes 1-2), 3′-flap DNA (lanes 3-4), 5′-pseudo Y DNA (lanes 5-6), and 3′-pseudo Y DNA (lanes 7-8). M represents DNA markers. (C) Diagrams of the major DNA cleavage sites catalyzed by Metnase. Arrows mark the major cleavage sites from the ³²P-labeled (*) 5′-end (calculated from the cleavage products shown in Fig. 3). The length of the arrows approximately was proportional to the intensity of resulting cleavage products.

(A) Metnase preferentially cleaves ssDNA overhang of flap and pseudo Y DNA. Wt-Metnase (0 or 50 ng) was incubated with 100 fmol of 5′-P³²-labeled DNA substrate indicated on the top (see Table 1 for the details of individual substrates) for 60 min prior to 12% denatured PAGE (+ 8M urea) analysis. Lanes “M” represent DNA markers. (B) Metnase exhibits both 3′- and 5′-ssDNA overhang cleavage activity. Metnase (0 or 50 ng) was incubated with 5′-flap DNA (lanes 1-2), 3′-flap DNA (lanes 3-4), 5′-pseudo Y DNA (lanes 5-6), and 3′-pseudo Y DNA (lanes 7-8). M represents DNA markers. (C) Diagrams of the major DNA cleavage sites catalyzed by Metnase. Arrows mark the major cleavage sites from the ³²P-labeled (*) 5′-end (calculated from the cleavage products shown in Fig. 3). The length of the arrows approximately was proportional to the intensity of resulting cleavage products.