Discovery of a Predicted DNA Knot Substantiates a Model for Site-Specific Recombination

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Abstract
The mechanism of site-specific genetic recombination mediated by Tn3 resolvase has been investigated by a topological approach. Extrapolation of a detailed model of synapsis and strand exchange predicts the formation of an additional DNA product with a specific knotted structure. Two-dimensional gel electrophoresis of DNA reacted in vitro revealed a product, about 0.1 percent of the total, with the appropriate mobility. A technique for determining DNA topology by electron microscopy was improved such that less than a nanogram of DNA was required. The structure of the knot was as predicted, providing strong evidence for the model and showing the power of the topological method.