Diffusion of knots in DNA molecules confined in nanochannels

Knots formed in DNA influence biological processes (e.g., DNA replication) and the accuracy of genomics technologies. Knot diffusion, which destroys knots in linear DNA molecules when the knot reaches the chain end, is a key step to understanding these processes. We present experimental data on the diffusion of knots in single DNA molecules via a combination of a nanofluidic "knot factory" device and fluorescence microscopy. Knots are first generated using pressure-driven flow, which compresses single DNA molecules against slit barriers in nanochannels. The knots are identified as bright spikes in intensity profiles of DNA backbone and their motions are tracked for 8 minutes. The ensembled-averaged data for the mean-squared displacement produce a scaling exponent that indicates that confined knots undergo subdiffusion. This result supports the theory that the knot breathing mechanism, where knot diffusion originates from a local motion of knot region, dominates knot diffusion in long polymer chains.