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bioRxiv · 10.64898/2026.09.20.753066

Breaking Pore Symmetry to Prolong DNA Residence in Solid-State Nanopores

Nasa, S.·Sur, P.·Maiti, P. K.·Varma, M.
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Abstract

Rapid DNA transport limits the temporal resolution of solid-state nanopore sensing. Here we show that breaking pore symmetry through geometric inclination produces exceptionally prolonged DNA residence without surface functionalization or external trapping. For 500-base-pair double-stranded (ds) DNA ,13 nm diameter SiNx pores in tilted membranes exhibit a distinct long-lived population with a mean dwell time of 11.1 seconds at 600 mV bias, exceeding previously reported dsDNA dwell times by at-least 4 orders of magnitude. Controlled pore tilting reproduces the population of prolonged events, whose prevalence and duration depend on ionic strength. TEM-EELS based thickness measurements exclude substantial membrane-thickness differences, while continuum and atomistic simulations support a mechanism coupling electric-field redistribution to off-axis DNA motion, increased pore-wall contact and suppressed axial mobility. These findings establish geometric inclination as a passive design variable for engineering molecular residence in solid-state nanopores and provide a route towards longer observation windows for single-molecule sensing.

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Nasa, S., Sur, P., Maiti, P. K., Varma, M.. 2026-09-22. Breaking Pore Symmetry to Prolong DNA Residence in Solid-State Nanopores. https://doi.org/10.64898/2026.09.20.753066

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