Amplifiable ratiometric fluorescence biosensing of nanosilver multiclusters populated in three-way-junction DNA branches

Target-Responsive Conformation Switch of Bihairpin Molecular Beacon to Illustrate Ratiometric Fluorescence Biosensing of Dual-Emissive Silver Nanoclusters

It might be intriguing to explore the tailored ability of a bihairpin-structured molecular beacon (bhMB) for improving reaction kinetics and assay sensitivity for a label-free ratiometric fluorescence assay of a specific trigger (T*), in which red and green silver nanoclusters (rSNC and gSNC) were utilized as two reverse emitting reporters. Unlike traditional dually labeled MB, herein the proposed bhMB was designed with two hairpin subunits for specific recognition and signaling readout. Four functional modules were included: the complement of T* in the identifiable hairpin, the template sequence of rSNC and gSNC in the signaling hairpin, two variable consensus loops capable of complementarily hybridizing to form one paired stem, and two stems able to merge into one new loop. Upon introducing T*, the conformation switch of bhMB was triggered via affinity linking to a cognate consensus sequence, thereby reconstructing a perfect stem-loop monohairpin structure. As such, the mutual transition of loops and stems between nonbinding and binding states was powered by a population-shift mechanism to shift the thermodynamic equilibrium toward the binding state. Benefiting from the structure confinement of bhMB, the local concentration of reactive species was increased to speed up the reaction kinetics. In a tailored response route, the template sequence for rSNC clustering was merged with increased red fluorescence, while the emission of gSNC was decreased, pointing to the obtained specific and sensitive ratiometric signal via built-in correction. Thus, this label-free strategy would be the first example to integrate recognizing and signaling subunits in a double-hairpin beacon for label-free biosensing and potential applications.

A bivariate fluorescence biosensor based on Janus DNA nanoarchitecture-loaded dual-emissive Ag nanoclusters as bi-responsive signaling reporters

Constructing label-free bivariate fluorescence biosensor would be intriguing and desired for the recognizable and accurate detection of two specific DNA segments, yet the design of functional DNA structures with low overlapped interference might be challenging. Herein in this work, a double-faced Janus DNA nanoarchitecture (JDNA) with bi-responsive recognition regions on opposite sides was assembled, which consisted of two substrate strands and two template strands for loading green-/red-emissive Ag nanoclusters (gAgNC and rAgNC) as bivariate signaling reporters. Of note, the hybridized double helix in the middle rationally oriented two flank faces and stabilized the rigid conformation of JDNA, while the template sequences of bicolor clusters were blocked to minimize non-specific background leakage. Upon inputting two targets, the discernible hairpins lost their hairpin structures due to forming two dsDNA complexes. They were executed to simultaneously invade JDNA for activating two individual target-recycled strand displacement (TRSD) events, guiding signal transduction and efficient amplification. Consequently, the clustering templates were unlocked via the tailored conformation switch of JDNA, in which gAgNC and rAgNC were in situ synthesized in two diagonal positions, thereby significantly emitting bi-responsive signal without cross interference. Benefited from the logic integration of double-faced JDNA and TRSD, a label-free, sensitive and specific bivariate fluorescence approach was developed, which would open a new avenue for the potential application in biosensing and bioanalysis.

Stimulus-Responsive Four-Stranded DNA Nanoring Assembly to Host Multiple Nanosilver Clusters for Cooperatively Enhanced Fluorescence Biosensing

Exploring the ability of four-stranded DNA nanorings (fsDNRs) to host multiple nanosilver clusters (NAgCs) for cooperatively amplifiable fluorescence biosensing to a specific initiator (tI*) is fascinating. By designing three DNA single strands and three analogous stem-loop hairpins, we developed a functional fsDNR through sequential cross-opening and overlapped hybridization. Note that a substrate strand (SS) was programmed with six modules: two severed splits (sT and sT') of NAgCs template, two sequestered segments by a middle unpaired spacer, and a partition for tI*-recognizable displacement, while sT and sT' were also tethered in two ends of three hairpins. At first, a triple dsDNA complex with stimulus-responsiveness was formed to guide the specific binding to tI*, while the exposed toehold of the SS activated the forward cascade hybridization of three hairpins, until the ring closure in the tailored self-assembly pathway for forming the fsDNR. The resulting four duplexes forced each pair of sT/sT' to be merged as the parent template in four nicks, guiding the preferential synthesis of four clusters in the shared fsDNR, thereby cooperatively amplifying the green fluorescence signal for sensitive assay of tI*. Meanwhile, the topological conformation of fsDNR can be stabilized by the as-formed cluster adducts to rivet the pair of two splits in the nicks. Benefitting from the self-enhanced effect of multiple emitters, this label-free fluorescent sensing strategy features simplicity, rapidity, and high on-off contrast, without involving complicated nucleic acid amplifiers.

Fluorescent DNA-Silver nanoclusters in food safety detection: From synthesis to application

In recent years, the conventional preparation of silver nanoclusters (AgNCs) has attracted much attention due to their ultra-small size, tunable fluorescence, easy-to-engineer, as well as biocompatible material. Moreover, its great affinity towards cytosine bases on single-stranded DNA has led to the construction of biosensors, especially aptamers, for a broad variety of applications in food safety and environmental protection. In past years, numerous researchers paid attention to the construction of AgNCs aptasensor. Therefore, this review will be an effort to summarize the synthetic strategy along with the influences of factors on synthesis, categorize the sensing mechanism of aptamer-functionalized AgNCs biosensors, as well as their specific applications in food safety detection including heavy metal, toxin, and foodborne pathogenic bacteria. Furthermore, a brief conclusion and outlook regarding the prospects and challenges of their applications in food safety were drawn in line with the developments in DNA-AgNCs.

Fluorescence Biosensing Based on Bifurcated DNA Scaffold-Aggregated Ag Nanocluster via Responsive Conformation Switch of Quasi-Molecular Beacon

To address the limitations of typical hairpin-structural molecular beacons, exploring the ability of a quasi-molecular beacon (qMB) to create label-free fluorescence biosensors is intriguing and remains a challenge. Herein, we propose the first example of modular qMB with the feature of a stimulation-responsive conformation switch to develop an aggregated Ag nanocluster (aAgNC) in a bifurcated DNA scaffold for fluorescently sensing a specific initiator (I*). This qMB was well designed to program four functional modules: I*-recognizable element adopting metastable stem-loop bihairpin structure and two DNA splits (exposed C3GT4 and locked C4AC4T) of aAgNC template that is separated by a tunable hairpin spacer for the customized combination of selective recognition and signaling readout. When presenting I* in an assay route, the specific hybridization induces the directional disassembly of the bihairpin unit, on which the qMB is configurationally switched to liberate the locked split. Thus, the bifurcated parent template pair of C3GT4/C4AC4T is proximal, affording in situ nucleation and clustering of emissive aAgNC. By collecting the fluorescence signal, the quantitative detection of I* is achieved. Benefiting from the ingenious programming of qMB, the recognizing and signaling integration actuates the construction of a facile and convenient fluorescent biosensor featuring rapid reaction kinetics, a wide linear range, high sensitivity, and specificity. This would provide a new paradigm to exploit versatile qMB-based biosensing platforms via stimulation-responsive conformation switches for developing various DNA-scaffolded Ag clusters.

Ratiometric Fluorescence Biosensing of Tandem Biemissive Ag Clusters Boosted by Confined Catalytic DNA Assembly

The reaction kinetics and yield of traditional DNA assembly with a low local concentration in homogeneous solution remain challenging. Exploring confined catalytic DNA assembly (CCDA) is intriguing to boost the reaction rate and efficacy for creating rapid and sensitive biosensing platforms. A rolling circle amplification (RCA) product containing multiple tandem repeats is a natural scaffold capable of guiding the periodic assembly of customized functional probes at precise sites. Here, we present a RCA-confined CCDA strategy to speed up amplifiable conversion for ratiometric fluorescent sensing of a sequence-specific inducer (I*) by using string green-/red-Ag clusters (sgAgCs and srAgCs) as two counterbalance emitters. Upon recognition of I*, CCDA events are operated by two toehold-mediated strand displacements and localized in repetitive units, thereby releasing I* for recycled signal amplification in the as-grown RCA concatemer. The local concentration of reactive species is increased to facilitate rapider dsDNA complex assembly and more efficient input-output conversion, on which the clustering template sequences of sgAgCs and srAgCs are blocked and opened, enabling srAgCs synthesis but opposite to sgAgCs. Thus, the fluorescence emission of srAgCs goes up, while sgAgCs go down. With the resultant ratio featuring inherent built-in correction, rapid, sensitive, and accurate quantification of I* at the picomolar level is achieved. Benefiting from efficient RCA confinement to enhance reaction kinetics and conversion yield, this CCDA-based strategy provides a new paradigm for developing simple and diverse biosensing methodologies.

Homogeneous Dual Fluorescence Count of CD4 in Clinical HIV-Positive Samples via Parallel Catalytic Hairpin Assembly and Multiple Recognitions

Regularly measuring the level of CD4+ cells is necessary for monitoring progression and predicting prognosis in patients suffering from an infection with the human immunodeficiency virus (HIV). However, the current flow cytometry standard detection method is expensive and complicated. A parallel catalytic hairpin assembly (CHA)-assisted fluorescent aptasensor is reported for homogeneous CD4 count by targeting the CD4 protein expressed on the membrane of CD4+ cells. Detection was achieved using CdTe quantum dots (QDs) and methylene blue (MB) as signal reporters. CdTe QDs distinguished CHA-assisted release of Ag+ and C-Ag+-C and MB that has differentiated cytosine (C)-rich single-stranded DNA (ssDNA) and C-Ag+-C, generating changes in fluorescence intensity. With the assistance of the CHA strategy and luminescent nanomaterials, this method reached limits of detection of 0.03 fg/mL for the CD4 protein and 0.3 cells/mL for CD4+ cells with linear ranges of 0.1 to 100 fg/mL and 1 to 1000 cells/mL, respectively. The method was validated in 50 clinical whole blood samples consisting of 30 HIV-positive patients, 10 healthy volunteers, and 10 patients with cancer or other chronic infections. The findings from this method were in good agreement with the data from clinical flow cytometry. Due to its sensitivity, affordability, and ease of operation, the current method has demonstrated great potential for routine CD4 counts for the management of HIV, especially in communities and remote areas.