How molecular knots can pass through each other.
We propose a mechanism in which two molecular knots pass through each other and swap positions along a polymer strand. Associated free energy barriers in our simulations only amount to a few kBT, which may enable the interchange of knots on a single DNA strand.
Department of Physics, Johannes Gutenberg University of Mainz, D-55128 Mainz, Germany; andGraduate School Materials Science in Mainz, D-55128 Mainz, Germany.
Benjamin
B
Trefz
Department of Physics, Johannes Gutenberg University of Mainz, D-55128 Mainz, Germany; and.
Jonathan
J
Siebert
Department of Physics, Johannes Gutenberg University of Mainz, D-55128 Mainz, Germany; and virnau@uni-mainz.de.
Peter
P
Virnau
D003201:Computers; D004247:DNA / Q000737:chemistry*; D004058:Diffusion; D008958:Models, Molecular; D049329:Nanostructures / Q000737:chemistry; D009690:Nucleic Acid Conformation; D011108:Polymers / Q000737:chemistry*; D013816:Thermodynamics
D011108:Polymers; D004247:DNA
diffusion; molecular dynamics