Figure 3.

Conformational changes induced by spermidine in Holliday junctions assembled with various combinations of proteins. (A) An EMSA using wild-type excision HJ substrates in the presence or absence of spermidine and the indicated proteins. IntF is the catalytically defective mutant Int Y342F protein. Multiple bands within a lane most likely indicate either alternate conformation of equivalent complexes and/or differing stoichiometries of Int. (B) KMnO₄ footprinting of the same excision HJ complexes shown in (A). In the upper gel are the labeled B′ OB strands of the junctions, while in the lower gel are shown the labeled BOC' strands of the junctions (see the schematic below the gels). The numbering of the bases is relative to the point of cleavage, where TS cleavage occurs between the bases at −3 and −2, while BS cleavage occurs between bases at +4 and +5.