A nanofluidic knot factory based on compression of single DNA in nanochannels

Susan Amin, Ahmed Khorshid, Lili Zeng, Philip Zimny and Walter Reisner ()
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Susan Amin: McGill University
Ahmed Khorshid: McGill University
Lili Zeng: McGill University
Philip Zimny: McGill University
Walter Reisner: McGill University

Nature Communications, 2018, vol. 9, issue 1, 1-10

Abstract: Abstract Knots form when polymers self-entangle, a process enhanced by compaction with important implications in biological and artificial systems involving chain confinement. In particular, new experimental tools are needed to assess the impact of multiple variables influencing knotting probability. Here, we introduce a nanofluidic knot factory for efficient knot formation and detection. Knots are produced during hydrodynamic compression of single DNA molecules against barriers in a nanochannel; 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 waiting time in the compressed state. Using a free energy derived from scaling arguments, we develop a knot-formation model that can quantify the effect of interactions and the breakdown of Poisson statistics at high compression. Our model suggests that highly compressed knotted states are stabilized by a decreased free energy as knotted contour contributes a lower self-exclusion derived free energy.

Date: 2018
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DOI: 10.1038/s41467-018-03901-w

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