Issue 30, 2016

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

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

Supplementary files

Article information

Article type
Paper
Submitted
12 maí 2016
Accepted
05 júl. 2016
First published
06 júl. 2016

Nanoscale, 2016,8, 14489-14496

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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