Handbook of Experimental Immunology

Abstract

The resolvase proteins encoded by transposons Tn3 and yb efficiently promote site-specific recombination of su-percoiled DNA containing directly repeated resolution (res) sites (1, 2). Distant sites are first brought together in an ordered fashion; the strands of this syn-apsed DNA are then broken in four locations, generating eight free ends, each of which undergoes defined reorientation and ligation. Such movements of recombining DNA strands often result in knotted or catenated products from whose structure it is possible to deduce critical features of a reaction pathway (3, 4). The fact that the topology of DNA knots or catenanes, unlike that of super-coils, is invariant in both intact and nicked duplex DNA has made electron microscopy particularly useful in analyzing these products of genetic rearrangement. No amount of stretching, twisting, or other physical distortion can alter the stereostructures of knotted or catenated products; the topological signature of the recombination mechanism remains distinct. The topological concepts used to analyze recombination are those of nodes and domains (5). Most easily defined for molecules viewed in plane projection, nodes are simply the crossings of DNA 12 JULY 1985 29.