The rate of sequencing or imaging is dependent on the mechanical movement speed of the magnetic beads, which is limited by drag force.  Currently, it is possible to measure 10 hairpin open-close cycle  per second.  Additional complications include the existence of a secondary hairpin structure in the DNA of interest.  In such a case the DNA loop to be ligated must be designed such that it its closing is favored over the closing of the endogenous loop in the DNA of interest.