Knot positioning in a copolymer with two different flexibilities
Numerical simulations show that the position of a knot in a ring flexible−stiff diblock copolymer depends on the length of each block and on temperature. When both blocks are sufficiently long to accommodate the knot, at low temperatures one finds the knot in the flexible part, while the knot migrates to the stiffer chain at higher temperatures. This is in agreement with recent findings by Likos and coworkers. In addition, we note that either interface between the two blocks is often found at one of the two extremities of the knot. Also a very short flexible region (i.e., a flexible defect of a stiff chain) is most likely within the knot at lower temperatures. Moreover, a knot can be trapped within a relatively short flexible region. These findings suggest that topoisomerases binding close to single-stranded gaps and nicks may effectively alter the global topology of the DNA.