Translation and untying of DNA knots in extensional fields

Knots occur naturally in biological DNA, a phenomenon relevant for cellular genome organization as well as genetic sequencing technology. Knotted DNA molecules serve as a model experimental system for polymer entanglement, where fluorescent microscopy can be used to study polymer dynamics on the individual chain level. To study the dynamics of knots in DNA, we induce knotting in viral DNA using an electrohydrodynamic instability and stretch the molecules with a divergent electric field in a microfluidic channel, analogous to elongational flow. The knots appear as bright spots of excess fluorescent intensity along the stretched molecule. With sufficiently long observation time, the knots are seen to translate along the molecule and eventually reach the chain ends and untie. The mobility of the knots can be controlled by modifying the applied strain rate, and can be jammed and re-started through step-function changes in the elongational field. The untying is a complex process that induces a temporary contraction of the molecule, which elongates as the knot unties, and produces several transient knots of lower topological complexity before completely untying.