(367a) Diffusion of Knotted DNA Molecules in Nanochannels in the Extended De Gennes Regime

Knots are intriguing topological objects, and the dynamical properties of knotted deoxyribonucleic acid (DNA) molecules are the subject of considerable work in the context of polymer physics and fluid mechanics. The effect of a knot on DNA diffusion in nanochannels in particular remains an open question. Two competing factors are expected to change the DNA friction in nanochannels due to the presence of knots. In the extended de Gennes regime of nanochannel confinement, DNA is a non-draining object whose friction is proportional to its extension along the channel axis. The formation of knots reduces the extension of the DNA chain confined in a nanochannel, thus decreasing the DNA friction. One potential counterbalancing effect is the increased friction between the channel wall and the knots. We measured center-of-mass diffusivity of nanochannel confined T4 DNA molecules before and after knot formation in the chains by a combination of a recently developed nanofluidic “knot factory” device for knot generation and fluorescence microscopy for knot detection. The chain diffusivity of knotted T4 DNA molecules is 0.014 ± 0.001 μm²/s, which is smaller than the unknotted DNA chain diffusivity of 0.0243 ± 0.0009 μm²/s. The reduced diffusivity due to the presence of knots indicates that the DNA-wall friction, rather than the shortening of DNA chains, dominates the knotted DNA diffusion in the extended de Gennes regime of nanochannel confinement.