The geometry of a synaptic intermediate in a pathway of bacteriophage lambda site-specific recombination

Bacteriophage lambda uses site-specific recombination to move its DNA into and out of the Escherichia coli genome. The recombination event is mediated by the phage-encoded integrase (Int) at short DNA sequences known as attac hment (att) sites. Int catalyzes recombination via at least four distinct p athways, distinguishable by their requirements for accessory proteins and b y the sequence of their substrates, The simplest recombination reaction cat alyzed by Int does not require any accessory proteins and takes place betwe en two attL sites. This reaction proceeds through an intermediate known as the straight-L bimolecular complex (SL-BMC), a stable complex which contain s two attL sites synapsed by Int. We have investigated the orientation of t he two substrates in the SL-BMC with respect to each other using two indepe ndent direct methods, a ligation assay and visualization by atomic force mi croscopy (AFM). Both show that the two DNA substrates in the complex are ar ranged in a tetrahedral or nearly square planar alignment skewed towards pa rallel. The DNA molecules in the complex are bent.