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Issue 30, 2016
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A universal design for a DNA probe providing ratiometric fluorescence detection by generation of silver nanoclusters

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Abstract

DNA-stabilized silver nanoclusters (AgNCs), the fluorescence emission of which can rival that of typical organic fluorophores, have made possible a new class of label-free molecular beacons for the detection of single-stranded DNA. Like fluorophore-quencher molecular beacons (FQ-MBs) AgNC-based molecular beacons (AgNC-MBs) are based on a single-stranded DNA that undergoes a conformational change upon binding a target sequence. The new conformation exposes a stretch of single-stranded DNA capable of hosting a fluorescent AgNC upon reduction in the presence of Ag+ ions. The utility of AgNC-MBs has been limited, however, because changing the target binding sequence unpredictably alters cluster fluorescence. Here we show that the original AgNC-MB design depends on bases in the target-binding (loop) domain to stabilize its AgNC. We then rationally alter the design to overcome this limitation. By separating and lengthening the AgNC-stabilizing domain, we create an AgNC-hairpin probe with consistent performance for arbitrary target sequence. This new design supports ratiometric fluorescence measurements of DNA target concentration, thereby providing a more sensitive, responsive and stable signal compared to turn-on AgNC probes. Using the new design, we demonstrate AgNC-MBs with nanomolar sensitivity and singe-nucleotide specificity, expanding the breadth of applicability of these cost-effective probes for biomolecular detection.

Graphical abstract: A universal design for a DNA probe providing ratiometric fluorescence detection by generation of silver nanoclusters

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Publication details

The article was received on 12 May 2016, accepted on 05 Jul 2016 and first published on 06 Jul 2016


Article type: Paper
DOI: 10.1039/C6NR03827A
Citation: Nanoscale, 2016,8, 14489-14496
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    A universal design for a DNA probe providing ratiometric fluorescence detection by generation of silver nanoclusters

    J. T. Del Bonis-O'Donnell, D. Vong, S. Pennathur and D. K. Fygenson, Nanoscale, 2016, 8, 14489
    DOI: 10.1039/C6NR03827A

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