Knots form when polymers self-entangle, a process enhanced by compaction with important implications in biological and artificial systems involving chain confinement. In this project we show that knots can be formed on single DNA molecules by compressing the chains against barriers in a nanochannel (“nanofluidic knot factory”). Subsequent extension of the chain enables direct assessment of the number of independently evolving knots. Knotting probability increases with chain compression as well as with how the chain is held in the compressed state.
Fig. 1 (a) Nanochannels with compression barrier. Molecules initially extended in the nanochannel (b) are compressed against the barrier (c) and then knots are observed once pressure is released and the DNA relaxes back to the extended conformation. (e) Kymographs indicating knot formation. (f). Knotting probability as a function of the compressed extension (red: probability of forming a state with one knot; blue: probability of forming a state with two knots; black: probability of forming a state with any number of knots).