(A) Nuclease assays were performed as in Fig. 2 except that the linearized 6.5 kb plasmid substrate was attached to a magnetic bead via a biotin/streptavidin linkage to the 5’ strand of the DNA distal to the probe region (see schematic at top). Assays were performed with 5.4 nM wild-type HerA, 38.4 nM wild-type NurA, and 6.6 nM wild-type MR as indicated for 30 min and analyzed in native agarose gels.
(B) Nuclease assays were performed as in (A) but the reaction products were analyzed using a probe specific for the 3’ strand adjacent to the 5’ biotin/bead (see schematic at top).