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arXiv · 2501.14347

Crowding Effects during DNA Translocation in Nanopipettes

Rand A. Al-Waqfi·Cengiz Khan·Oliver J. Irving·Lauren Matthews·Tim Albrecht
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Abstract

Quartz nanopipettes are an important emerging class of electric single-molecule sensors for DNA, proteins, their complexes as well as other biomolecular targets. However, in comparison to other resistive pulse sensors, nanopipettes constitute a highly asymmetric environment and the transport of ions and biopolymers can become strongly direction-dependent. For double-stranded DNA, this can include the characteristic translocation time and its tertiary structure, but as we show here, nanoconfinement can not only lead to unexplored features in the transport characteristics of the sensor, but also unlock new capabilities for biophysical and bioanalytical studies at the single-molecule level. To this end, we show how the accummulation of DNA inside the nanochannel leads to crowding effects, and in some cases reversible blocking of DNA entry, and provide a detailed analysis based on a range of different DNA samples and experimental conditions. Moreover, using biotin-functionalised DNA and streptavidin-modified gold nanoparticles as target, we demonstrate in a proof-of-concept study how the crowding effect, and the resulting increased residence time in nanochannel, can be exploited in a new analytical paradigm, involving DNA injection into the nanochannel, incubation with the nanoparticle target and analysis of the complex by reverse translocation. We thereby integrate elements of sample processing and detection into the nanopipette, as an important conceptual advance, and make a case for the wider applicability of this device concept.

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Rand A. Al-Waqfi, Cengiz Khan, Oliver J. Irving, Lauren Matthews, Tim Albrecht. 2025-01-24. Crowding Effects during DNA Translocation in Nanopipettes. https://arxiv.org/abs/2501.14347

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