Quantum dot-enhanced detection of dual short RNA sequences via one-step template-dependent surface hybridization

Subnanomolar FRET-Based DNA Assay Using Thermally Stable Phosphorothioated DNA-Functionalized Quantum Dots

Quantum dots (QDs) can serve as an attractive Förster resonance energy transfer (FRET) donor for DNA assay due to their excellent optical properties. However, the specificity and sensitivity of QD-based FRET analysis are prominently reduced by nonspecific DNA adsorption and poor colloidal stability during DNA hybridization, which hinders the practical applications of QDs as a biosensing platform. Here, we report subnanomolar FRET assay of DNA through the stabilization of DNA/QD interface using DNA-functionalized QDs with phosphorothioated single-stranded DNA (pt-ssDNA) as a multivalent ligand in an aqueous solution. In situ DNA functionalization was achieved during the aqueous synthesis of CdTe/CdS QDs, resulting in the maximum photoluminescence quantum yields of 76.9% at an emission wavelength of 732 nm. Conventional monothiolated ssDNA-capped QDs exhibited particle aggregation and photoluminescence (PL) quenching during DNA hybridization at 70 °C due to the dissociation of surface ligands. Such colloidal instability induced the nonspecific adsorption of DNA, resulting in false-positive signal and decreased sensitivity with the limit of detection (LOD) of 16.1 nM. In contrast, the pt-ssDNA-functionalized QDs maintained their colloidal stability and PL properties at elevated temperatures. The LOD of the pt-ssDNA-functionalized QDs was >30 times lower (0.47 nM) while maintaining the high specificity to a target sequence because the strong multivalent binding of pt-ssDNA to the surface of QDs prevents the detachment of pt-ssDNA and nonspecific adsorption of DNA. The study suggests that the ligand design to stabilize the surface of QDs in an aqueous milieu is critically important for the high performance of QDs for specific DNA assay.

Duplex-Specific Nuclease-Amplified Detection of MicroRNA Using Compact Quantum Dot-DNA Conjugates

Advances in nanotechnology have provided new opportunities for the design of next-generation nucleic acid biosensors and diagnostics. Indeed, combining advances in functional nanoparticles, DNA nanotechnology, and nuclease-enzyme-based amplification can give rise to new assays with advantageous properties. In this work, we developed a microRNA (miRNA) assay using bright fluorescent quantum dots (QDs), simple DNA probes, and the enzyme duplex-specific nuclease. We employed an isothermal target-recycling mechanism, where a single miRNA target triggers the cleavage of many DNA signal probes. The incorporation of DNA-functionalized QDs enabled a quantitative fluorescent readout, mediated by Förster resonance energy transfer (FRET)-based interaction with the DNA signal probes. Our approach splits the reaction in two, performing the enzyme-mediated amplification and QD-based detection steps separately such that each reaction could be optimized for performance of the active components. Target recycling gave ca. 3 orders of magnitude amplification, yielding highly sensitive detection with a limit of 42 fM (or 1.2 amol) of miR-148, with excellent selectivity versus mismatched sequences and other miRNAs. Furthermore, we used an alternative target (miR-21) and FRET pair for direct and absolute quantification of miR-21 in RNA extracts from human cancer and normal cell lines.

Duplex microRNAs assay based on target-triggered universal reporter hybridization

In this paper, we designed and evaluated a duplex detection strategy for microRNAs (miRNAs) using universal probe-based target-triggered double hybridization and fluorescent microsphere-based assay system (xMAP array). In the absence of target miRNA, reporter DNA cannot hybridize stably with the immobilized capture DNA due to its low melting temperature. Only after adding target miRNA, can reporter probe hybridize with capture probe to form a stable three-component complex. This target-triggered stable hybridization makes this method possible for highly selective and sensitive detection of multiple miRNAs. We exemplified a quantitative detection of duplex miRNAs with a limit of detection of 40 pM. The xMAP array platform holds the potential of extending this approach to simultaneous detection of up to 100 miRNA targets. Considering the simplicity, rapidity and multiplexing, this work promised a potential detection of multiple miRNA biomarkers for early disease diagnosis and prognosis.

Rapid and Multiplexed MicroRNA Diagnostic Assay Using Quantum Dot-Based Förster Resonance Energy Transfer

The detection of next generation microRNA (miRNA) biomarkers has become a highly important aspect for clinical diagnostics. We use multiplexed Förster resonance energy transfer (FRET) between a luminescent Tb complex and three different semiconductor quantum dots (QDs) to sensitively detect three different miRNAs from a single 150 μL sample with ca. 1 nM (subpicomol) detection limits. The rapid and amplification-free mix-and-measure assay format is based on careful design of miRNA base pairing and stacking to selectively detect different miRNAs with very strong sequence homologies. Clinical applicability is demonstrated by sensitive multiplexed quantification of three miRNAs at low (2 to 10 nM) and varying concentrations in samples that contained up to 10% serum.

Simultaneous and sensitive detection of dual DNA targets via quantum dot-assembled amplification labels

We describe a signal amplification assay for the simultaneous detection of HIV-1 and HIV-2 via a quantum dot (QD) layer-by-layer assembled polystyrene microsphere (PS) composite in a homogeneous format. The crucial point of this composite is the core-shell system. PS is utilized as the core and QDs as the shell. Based on the high affinity of streptavidin and biotin, QDs are assembled layer-by-layer on the surface of the PS as amplification labels. Biotinylated reporter probe is combined with the PS-QDs conjugate and then hybridized with target DNA immobilized on the surface of a 96-well plate. Using this approach, each target DNA corresponds to a large number of QDs and the fluorescence signal is greatly enhanced. Two QD colors (605 and 655 nm) are used to detect dual-target DNAs simultaneously. Taking advantage of the enzyme-free reaction and high sensitivity, this PS-QD-based sensor can be used in simple 'mix and detection' assays. Our results show that this technology has potential application in rapid point-of-care testing, gene expression studies, high-throughput screening and clinical diagnostics.

Nucleic acid/quantum dots (QDs) hybrid systems for optical and photoelectrochemical sensing

Nucleic acid/semiconductor quantum dots (QDs) hybrid systems combine the recognition and catalytic properties of nucleic acids with the unique photophysical features of QDs. These functions of nucleic acid/QDs hybrids are implemented to develop different optical sensing platforms for the detection of DNA, aptamer-substrate complexes, and metal ions. Different photophysical mechanisms including fluorescence, electron transfer quenching, fluorescence resonance energy transfer (FRET), and chemiluminescence resonance energy transfer (CRET) are used to develop the sensor systems. The size-controlled luminescence properties of QDs are further implemented for the multiplexed, parallel analysis of several DNAs, aptamer-substrate complexes, or mixtures of ions. Similarly, methods to amplify the sensing events through the biocatalytic regeneration of the analyte were developed. An additional paradigm in the implementation of nucleic acid/QDs hybrids for sensing applications involves the integration of the systems with electrodes, and the generation of photocurrents as transduction signals for the sensing events. Finally, semiconductor QDs conjugated to functional DNA machines, such as "walker" systems, provide an effective optical label for probing the dynamics and mechanical functions of the molecular devices. The present article addresses the recent advances in the application of nucleic acid/QDs hybrids for sensing applications and DNA nanotechnology, and discusses future perspectives of these hybrid materials.

Sensitive chemiluminescence aptasensor based on exonuclease-assisted recycling amplification

We report herein an exonuclease-assisted aptamer-based target recycling amplification strategy for sensitive and selective chemiluminescence (CL) determination of adenosine. This aptasensor is based on target-induced release of aptamers from capture probes immobilized on the 96-well plate surface, and thus leading to a decreased hybridization with gold nanoparticle-functionalized reporter sequences followed by a CL signal. The introduction of exonuclease III catalyzes the stepwise removal of mononucleotides from 3'-hydroxyl termini of duplex DNAs of aptamers, liberating the adenosine. Therefore, a single copy of target adenosine can lead to the release and digestion of numerous aptamer strands from the 96-well plates and ultimately an enhanced sensitivity is achieved. Experimental results revealed that the exonuclease-assisted recycling strategy enabled the monitoring of adenosine with wide working ranges and low detection limits (LOD: 0.5 nM). This new CL strategy might create a novel technology for the detection of various targets and could find wide applications in the environmental and biomedical fields.