How knots can swap positions on a DNA strand
Physicists of the Johannes Gutenberg-University and the Graduate School Mainz (B. Trefz, J. Siebert and P. Virnau) confirmed and explained a mechanism, by which two knots on a DNA strand can interchange their positions. One of the knots grows in size while the other diffuses along the contour of the former (as shown in the schematic picture). By using molecular dynamics simulation a significant number of crossing events were observed in order to estimate the free energy barrier of the swap. As the barrier in the free energy is rather small, the mechanism could not only take place in vivo, but may also play an important role in future technologies such as nanopore sequencing, where long DNA strands are sequenced by being pulled though pores.
This work was published in PNAS 111 (22), 7948-7951 (2014).
Figure caption: Schematic representation of the swapping event. One of the knots grows in size, while the other diffuses along the contour of the former. (This picture was adapted from Fig.1 of the publication.)