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A versatile single-molecule counting-based platform by generation of fluorescent silver nanoclusters for sensitive detection of multiple nucleic acids

Abstract

The good photostability and strong brightness of individual DNA-templated silver nanoclusters (DNA-AgNCs) have been confirmed by single-molecule imaging in this work and DNA-AgNCs as a new class of outstanding fluorophores are applied in the construction of single-molecule counting-based probes for the first time. Based on the fluorescent AgNC-generating molecular beacons (AgNC-MBs), we present a versatile method for simultaneous analysis of multiple nucleic acids. Distinct from previous designs that a AgNC stabilizing sequence is incorporated into the stem of a hairpin DNA to form the AgNC-MB, we prepared a nicked MB that the AgNC stabilizing sequence is hybridized with the longer stem of a single-stranded DNA (ssDNA) with stem-loop structure. Our proposed AgNC-MB is activated by the probe-target hybridization then releases the AgNC stabilizing sequence via toehold-mediated strand displacement reaction, the versatility of which has been greatly improved because bases in the target-binding region are not involved in the forming of DNA-AgNCs. As a proof of concept, the simultaneous detection of two breast cancer-related MicroRNAs (miR-21 and let-7a miRNA) has been achieved with total internal reflection fluorescence (TIRF)-based imaging and the detection sensitivity of our method has been demonstrated to be improved by at least two orders of magnitude compared with conventional AgNC-MBs. Furthermore, in the single-nucleotide mutation identification assay, the simultaneous detection strategy introduces a competitive reaction between the two probe-target hybridizations, resulting in the excellent discrimination ability of AgNC-MB sensing platform and the mutant-type targets can be successfully detected at a low abundance. The new AgNC-MB sensing platform demonstrated a potential to make AgNCs an attractive alternative to conventional organic dyes for single-molecule studies.

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Supplementary files

Publication details

The article was received on 30 May 2019, accepted on 07 Aug 2019 and first published on 08 Aug 2019


Article type: Paper
DOI: 10.1039/C9NR04608A
Nanoscale, 2019, Accepted Manuscript

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    A versatile single-molecule counting-based platform by generation of fluorescent silver nanoclusters for sensitive detection of multiple nucleic acids

    M. Peng, Z. Fang, N. Na and J. Ouyang, Nanoscale, 2019, Accepted Manuscript , DOI: 10.1039/C9NR04608A

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