Diffusion of knotted DNA molecules in nanochannels

Knots are intriguing topological objects and have been the focus of considerable study in the context of polymer physics. The effect of knot formation on diffusion of DNA confined in nanochannels in particular remains an open question. Two competing factors are expected to affect the change in friction of the confined DNA due to the presence of knots. Under the de Gennes regime in nanochannel confinement, the DNA is a non-draining object whose friction is proportional to its size, thus the formation of knots decreases the friction. The counteracting effect is the increased friction between the DNA and channel surface. Here, we present experimental data on the diffusion of T4 DNA before and after knot formation via a combination of a nanofluidic “knot factory” device for knot generation and fluorescence microscopy for DNA observation. We will discuss the measured diffusivity of unknotted and knotted T4 DNA molecules which will address this question, which competing effects dominates the knotted DNA diffusion in nanochannels.