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Issue 35, 2019
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Fast capture and multiplexed detection of short multi-arm DNA stars in solid-state nanopores

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Abstract

Fast and multiplexed detection of low-abundance disease biomarkers at the point-of-need would transform medicine. Nanopores have gained attention as single-molecule counters to electrically detect a range of biological molecules in a handheld format, but challenges remain before diagnostic applications can emerge. For solid-state nanopore sensors, the specificity of the ionic current signatures and the rate of target capture required to simultaneously recognize and rapidly count a mixture of molecular targets in a complex sample are active areas of research. Herein, we study the capture and translocation characteristics of short N-arm star shaped DNA nanostructures to evaluate their potential as a family of surrogate label molecules for biomarkers of interest, designed for fast and reliable multiplexed detection based on conductance blockages. Simple hybridization of a varying number of short, easily synthesized 50 bp ssDNA strands allows the number of arms in the star shape DNA to be controlled from N = 3 to 12. By introducing more arms to the nanostructures, we show that we can controllably increase the nanopore signal-to-noise ratio for a range of pore sizes, producing conductance blockages which increase linearly with the number of arms, and we demonstrate conductance-based multiplexing through simultaneous detection of three such nanostructures. Moreover, the increased molecular signal strength facilitates detection under salt concentration asymmetries, allowing for a capture rate enhancement of two orders of magnitude without compromising the nanopore temporal and ionic signals. Together, these attributes (strong signal, multiplexing potential and increased counting rate) make the N-arm star DNA-based nanostructures promising candidates as proxy labels for the detection of multiple biomarkers of interest in future high sensitivity single-molecule solid-state nanopore-based assays.

Graphical abstract: Fast capture and multiplexed detection of short multi-arm DNA stars in solid-state nanopores

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Supplementary files

Article information


Submitted
29 May 2019
Accepted
29 Jul 2019
First published
02 Aug 2019

Nanoscale, 2019,11, 16342-16350
Article type
Paper

Fast capture and multiplexed detection of short multi-arm DNA stars in solid-state nanopores

L. He, P. Karau and V. Tabard-Cossa, Nanoscale, 2019, 11, 16342
DOI: 10.1039/C9NR04566J

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