Detecting topological variations of DNA at single-molecule level

Ke Liu (), Chao Pan, Alexandre Kuhn, Adrian Pascal Nievergelt, Georg E. Fantner, Olgica Milenkovic and Aleksandra Radenovic ()
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Ke Liu: EPFL
Chao Pan: University of Illinois at Urbana-Champaign
Alexandre Kuhn: University of Lausanne
Adrian Pascal Nievergelt: EPFL
Georg E. Fantner: EPFL
Olgica Milenkovic: University of Illinois at Urbana-Champaign
Aleksandra Radenovic: EPFL

Nature Communications, 2019, vol. 10, issue 1, 1-9

Abstract: Abstract In addition to their use in DNA sequencing, ultrathin nanopore membranes have potential applications in detecting topological variations in deoxyribonucleic acid (DNA). This is due to the fact that when topologically edited DNA molecules, driven by electrophoretic forces, translocate through a narrow orifice, transient residings of edited segments inside the orifice modulate the ionic flow. Here we utilize two programmable barcoding methods based on base-pairing, namely forming a gap in dsDNA and creating protrusion sites in ssDNA for generating a hybrid DNA complex. We integrate a discriminative noise analysis for ds and ss DNA topologies into the threshold detection, resulting in improved multi-level signal detection and consequent extraction of reliable information about topological variations. Moreover, the positional information of the barcode along the template sequence can be determined unambiguously. All methods may be further modified to detect nicks in DNA, and thereby detect DNA damage and repair sites.

Date: 2019
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DOI: 10.1038/s41467-018-07924-1

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