  We develop topological methods for analyzing difference topology experiments
involving 3-string tangles. Difference topology is a novel technique used to
unveil the structure of stable protein-DNA complexes involving two or more DNA
segments. We analyze such experiments for the Mu protein-DNA complex. We
characterize the solutions to the corresponding tangle equations by certain
knotted graphs. By investigating planarity conditions on these graphs we show
that there is a unique biologically relevant solution. That is, we show there
is a unique rational tangle solution, which is also the unique solution with
small crossing number.
