Multiplexed Analysis of Genes Using Nucleic Acid-Stabilized Silver-Nanocluster Quantum Dots

Abstract

Luminescent nucleic acid-stabilized Ag nanoclusters (Ag NCs) are applied for the optical detection of DNA and for the multiplexed analysis of genes. Two different sensing modules including Ag NCs as luminescence labels are described. One sensing module involves the assembly of a three-component sensing module composed of a nucleic acid-stabilized Ag NC and a quencher-modified nucleic acid hybridized with a nucleic acid scaffold that is complementary to the target DNA. The luminescence of the Ag NCs is quenched in the sensing module nanostructure. The strand displacement of the scaffold by the target DNA separates the nucleic acid-functionalized Ag NCs, leading to the turned-on luminescence of the NCs and to the optical readout of the sensing process. By implementing two different-sized Ag NC-modified sensing modules, the parallel multiplexed analysis of two genes (the Werner Syndrome gene and the HIV, human immunodeficiency, gene), using 615 and 560 nm luminescent Ag NCs, is demonstrated. The second sensing module includes the nucleic acid functionalized Ag NCs and the quencher-modified nucleic acid hybridized with a hairpin DNA scaffold. The luminescence of the Ag NCs is quenched in the sensing module. Opening of the hairpin by the target DNA triggers the luminescence of the Ag NCs, due to the spatial separation of the Ag NCs/quencher units. The system is applied for the optical detection of the BRAC1 gene. In addition, by implementing two-sized Ag NCs, the multiplexed analysis of two genes by the hairpin sensing module approach is demonstrated.

Progress in miRNA Detection Using Graphene Material–Based Biosensors

“…Owing to interaction of target analyte with probe molecule modified with an optically active receptor (dye‐label, fluorescent silver clusters, or quantum dots), optical biosensors designed for all kinds of external stimulus detection will transduce the optical signal in the form of absorbance or fluorescence depending on the distance between fluorescent probe and quenching agent. By taking the advantage of this interesting phenomenon, Willner's group did many excellent works . For example, as H 2 O 2 and quinones could induce the effective quenching of the fluorescent silver nanoclusters (AgNCs), the DNA‐stabilized AgNCs were used to act as fluorescent labels for probing biocatalytic transformations of different enzyme systems (glucose oxidase and tyrosinase) and following the biocatalyzed reactions of enzyme cascades (the alkaline phosphatase/tyrosinase cascade and the acetylcholinesterase/choline oxidase cascade) .…”

A label-free and enzyme-free ultra-sensitive transcription factors biosensor using DNA-templated copper nanoparticles as fluorescent indicator and hairpin DNA cascade reaction as signal amplifier

“…Among these biomolecules, oligonucleotide represents particularly good template candidate due to the unique nanosized structure, excellent programmable properties, and rich functional groups including heterocyclic nitrogen atoms, amino groups, and phosphate groups, which can bind with specific metal ions and provide nucleation sites for metallic nanoparticles. Nucleic acid-templated fluorescent metal nanoparticles have been intensely investigated in the past decade, such as gold nanoclusters (Au NCs) (Kennedy et al, 2012;Teng et al, 2015), silver nanoclusters (Ag NCs) (Richards et al, 2008;Enkin et al, 2014), and copper nanoparticles (Cu NPs) (Rotaru et al, 2010;Qing et al, 2013a). These DNA templated inorganic nanoparticles have the potential to be a label-free fluorescent indicator with mild reaction conditions and high efficiencies due to the fact that DNA are usually involved in the whole reaction system and strongly correlated to the target analytes.…”

A novel linear molecular beacon based on DNA-scaffolded silver nanocluster for DNA detection via exonuclease III-assisted cyclic amplification

“…From this sizedependent standpoint, the unique optical and electrical functionalities of nanoclusters have the potential to produce electronic properties compare to much larger nanoparticles owing to the presence of molecule-like discrete energy levels. 8-10 DNA/AgNCs as fluorescent biolabels have enabled applications ranging from detection of various analytes, including metal ions, [11][12] nucleic acid, [13][14][15][16] and enzyme activity in biocatalysis, [17][18] to design of complex nanostructures [19][20] and logic gates. 6 Particularly, the creation of water-soluble DNA-scaffolded AgNCs (DNA/AgNCs) by binding silver ions to bases (mainly cytosine) and adding a reducing agent have attracted considerable attention.…”