Figure 6.

RMS motions for different loop topologies. The 180° and 360° loop topologies trapped by FokI on the IF and DF construct result in a lower RMS motion on the IF species compared to the DF species. This is due to the additional 180° bend outside of the loop trapped on the IF DNA that is not present with the 360° loop topology generated on the DF DNA. The net result is that the average end-to-end length of the tether is shorter with the IF DNA than with the DF DNA, thus positioning its bead closer to the glass slide. Dotted lines reflect RMS motion.