Preparation of figure 8 and cruciform DNAs and their use in studies of the kinetics of branch migration.

We have re-examined the kinetics of the branch migration of double-stranded DNA that is mediated by the stepwise movement of the Holliday junction. This work revises and extends our previous treatment (Thompson, B. J., Camien, M. N., and Warner, R. C. (1976) Proc. Natl. Acad. Sci. U.S.A. 73, 2299-2303). New methodology and new highly purified substrates have been used. The latter include figure 8s prepared from phage G4 DNA by annealing single-stranded components and two sizes of a novel cruciform. We treat the process as a one-dimensional diffusion based on the random walk, the mathematical basis of which is discussed in detail. The step rate is shown to be 3 orders of magnitude slower than we reported previously. The most important contribution to the erroneously high rate was a result of the presence of EDTA in the spreading solution used for electron microscopy at that time. A second contribution of about 4-fold resulted from catalysis by EcoRI and other proteins. The rates reported here are for the uncatalyzed reaction.