The First FRET-Based RNA Aptamer NanoKit for Sensitively and Specifically Detecting c-di-GMP

An effective method to identify c-di-GMP may significantly facilitate the exploration of its signaling pathways and bacterial pathogenesis. Herein, we have developed the first conjugated polymer-amplified RNA aptamer NanoKit with a unique core-shell-shell architecture, which combines the advantages of high selectivity of RNA aptamers and high sensitivity of strong fluorescence resonance energy transfer (FRET) effect, for precisely detecting c-di-GMP. We identified that NanoKit could selectively detect c-di-GMP with a low detection limit of 50 pM. Importantly, NanoKit could identify bacterial species and physiological states, such as planktonic, biofilm, and even antibiotic-resistance, on the basis of their different c-di-GMP expression patterns. Particularly, NanoKit could distinguish bacterial infection and inflammation and identify Pseudomonas aeruginosa associated pneumonia and sepsis, thereby guiding treatment choice and monitoring antibiotic effects. Therefore, NanoKit provides a promising strategy to rapidly identify c-di-GMP and its associated diseases and may benefit for pathophoresis management.

Photocaged amplified FRET nanoflares: spatiotemporal controllable of mRNA-powered nanomachines for precise and sensitive microRNA imaging in live cells

There is considerable interest in creating a precise and sensitive strategy for in situ visualizing and profiling intracellular miRNA. Present here is a novel photocaged amplified FRET nanoflare (PAFN), which spatiotemporal controls of mRNA-powered nanomachine for precise and sensitive miRNA imaging in live cells. The PAFN could be activated remotely by light, be triggered by specific low-abundance miRNA and fueled by high-abundance mRNA. It offers high spatiotemporal control over the initial activity of nanomachine at desirable time and site, and a ‘one-to-more’ ratiometric signal amplification model. The PAFN, an unprecedented design, is quiescent during the delivery process. However, upon reaching the interest tumor site, it can be selectively activated by light, and then be triggered by specific miRNA, avoiding undesirable early activation and reducing nonspecific signals, allowing precise and sensitive detection of specific miRNA in live cells. This strategy may open new avenues for creating spatiotemporally controllable and endogenous molecule-powered nanomachine, facilitating application at biological and medical imaging.

Logic-signal-based multiplex detection of MiRNAs with high tension hybridization and multiple signal amplification

A multiplex miRNA detection scheme with simultaneous multiple signal output by single excitation has been reported.

Photocaged FRET nanoflares for intracellular microRNA imaging

Herein, we developed photocaged FRET nanoflares for spatiotemporal microRNA imaging in living cells. In other words, the probes will not work until they are exposed to UV light.

MicroRNA Detection with Turnover Amplification via Hybridization-Mediated Staudinger Reduction for Pancreatic Cancer Diagnosis

The occurrence of and development in the early pathological stage of pancreatic cancer has proved to be associated with microRNAs. However, it remains a great challenge to directly monitor low-expression, and downregulation of, microRNA among living cells, tissues, and serum samples. In this work, Staudinger reduction is first applied in intracellular microRNA detection, establishing a set of smart hybridization-mediated Staudinger reduction probes (HMSR-probe) which contain designed oligonucleotide sequences. Meanwhile, 40 serum samples (healthy people (6), patients with pancreatitis (22), and pancreatic cancer patients (12)) are tested for exploring the potential clinical application. Of note, the molecules bound to nucleic acid confine the reactive site to close proximity in a compact space, and nonconnected product from Staudinger reaction facilitates turnover amplification to an ameliorative detection limit (1.3 × 10^-15 M). Moreover, compared with qRT-PCR, a low false positive signal and an excellent specificity makes the probe more suitable and convenient for pancreatic cancer diagnosis in blood samples. For practical applications, HMSR-probe enable accurate differentiation in cell and tissue samples under both 488 and 785 nm and have good coherence to known research. As a proof of concept, the reliable results in distinguishing pancreatic cancer patients from different morbid stages might supply a feasible method for endogenous microRNA detection in fundamental research and clinical diagnostics.

Versatile Electrochemiluminescence and Photoelectrochemical Detection of Glutathione Using Mn2+ Substitute Target by DNA-Walker-Induced Allosteric Switch and Signal Amplification

Glutathione (GSH) serves vital functions in biological systems and associates with various human diseases. In this work, a versatile electrochemiluminence (ECL) and a photoelectrochemical (PEC) "signal on" biosensing platform were developed for a sensitive assay of GSH by a Mn²⁺-powered DNAzyme amplification strategy combined with DNA-walker-triggered allosteric conversion. First, MnO₂ nanosheets were reduced to Mn²⁺ by GSH; then, Mn²⁺ as a substitute target triggered DNAzyme-assisted cleavage-cycling amplification to generate numerous DNA output (s3). Meanwhile, the DNA molecular machine was introduced to bridge signal probes for versatile biosensing, which included hairpin DNA as a track and an arm as a walker. The presence of DNA output (s3) activated the swing arm to hybridize with hairpin DNA and then cut it by Nt.BbvCI, which initiated autonomous walking of the arm for forming a large number of streptavidin (SA) aptamers. Thus, a large number of CdS:Mn-SA tags as versatile signal probes was linked to the electrode by specific SA-aptamer binding, generating highly enhanced ECL and PEC signals for sensitive detection of the target. The present biosensing system take advantage of metal ion-based DNAzyme amplification, a DNA walker machine, multi-signals of QDs, and specificity of aptamers, which can provide a universal and efficient biosensing method for detecting various targets. The designed strategy demonstrated good performance for a GSH assay in human serum samples, showing more promising applications than other reported methods.

Paper-Supported Self-Powered System Based on a Glucose/O2 Biofuel Cell for Visual MicroRNA-21 Sensing

The exploitation of self-powered devices that get rid of the power source restriction represents the development tendency of sensing systems. Herein, a paper-supported glucose/O₂ biofuel cell (BFC)-based self-powered sensing platform for visual analysis was developed. The BFC device utilized gold nanoparticle-modified paper fibers as the electrode to wire glucose oxidase (GOx) and bilirubin oxidase for the fabrication of bioanodes and biocathodes. To implement an assay protocol, a target-responsive cargo release system based on mesoporous silica nanocarriers controlled by microRNA-21 (miRNA-21) was designed. During the BFC operation, undesired H₂O₂, the side product of glucose oxidation which would be deleterious for GOx, was generated, leading to inevitable degeneration of BFC performance. On the basis of the H₂O₂-mediated iodide oxidation reaction to form iodine that further modulated the starch chromogenic reaction, undesired H₂O₂ could be effectively removed, resulting in remarkably improved BFC performance as well as providing a means for visual signal readout. Thanks to the dual output signals (maximum power output density or length of blue bar), enhanced analysis reliability and sensitive detection of miRNA-21 over a range of 5 fM to 100 pM were achieved. Moreover, this study demonstrates a proof of concept in visualized BFC-based self-powered systems for sensing applications and provides a blueprint to advance future sensors and analysis devices powered by BFCs in a wide variety of in vitro applications.

Affinity-Modulated Molecular Beacons on MoS2 Nanosheets for MicroRNA Detection

DNA-functionalized layered two-dimensional transition-metal dichalcogenides have attracted tremendous interest for constructing biosensors in recent years. In this work, we report diblock molecular beacons with poly-cytosine (polyC) tails anchored on molybdenum disulfide (MoS₂) nanosheets as probes for microRNA detection. The polyC block is adsorbed on MoS₂ and the molecular beacon block is available for hybridization to the target; duplex-specific nuclease provides signal amplification by target recycling. By changing the length of polyC, we regulate the density of probes on MoS₂ and inhibit the adsorption of enzyme-cleaved oligonucleotides, thereby leading to higher quenching efficiency. PolyC-mediated molecular beacons on MoS₂ have very low background signal, ultrahigh sensitivity (limit of detection ∼3.4 fM), specificity to detect a single nucleotide mismatch, and selectivity to detect target microRNA from serum samples. This detection platform holds great potential for quantitative analysis of miRNAs in clinical diagnosis and biomedical research.

Multiplex microRNA imaging in living cells using DNA-capped-Au assembled hydrogels

Non-invasively imaging multiplex microRNAs (miRNAs) in living cells is pivotal to understanding their physiological functions and pathological development due to the key regulatory roles of miRNAs in gene expression. However, developing smart delivery systems with large gene loading capacity, biocompatibility and responsiveness remains a significant challenge. Herein, we successfully incorporated DNA-capped Au nanoparticles (NPs) and their complementary fluorescent DNA sequences into a porous 3D hydrogel network (AuDH), in which hairpin-locked DNAzyme strands and active metal ions were loaded (AuDH/M n+/H) for simultaneously imaging multiplex miRNAs in living cells. After transfection into cells, the specific miRNAs trigger the strand-displacement reaction and sequentially activate the DNAzyme-assisted target recycling, leading to a strong increase in the corresponding fluorescence intensity for imaging. This enables simultaneous assessment of the abundance of multiplex cancer-related miRNAs, even if at a very low expression level, in different cells through the different fluorescence intensities due to the dual signal amplification, and the change in abundance of miRNAs induced by siRNA or miRNA mimics in living cells can also be efficiently monitored. The versatile and responsive DNA hydrogel system holds great potential for miRNA biomedical applications.

A DNA-linker-DNA bifunctional probe for simultaneous SERS detection of miRNAs via symmetric signal amplification

In this work, using a dual functional DNA-linker-DNA (DLD) probe, a new concept of a symmetric signal amplification (SSA) reaction is introduced to simultaneously analyze miRNAs. By coupling the surface-enhanced Raman scattering (SERS) technology with symmetric amplification modes, this flexible biosensing system exhibits high sensitivity and specificity.

Universal, colorimetric microRNA detection strategy based on target-catalyzed toehold-mediated strand displacement reaction

In this work, we developed a novel, label-free, and enzyme-free strategy for the colorimetric detection of microRNA (miRNA), which relies on a target-catalyzed toehold-mediated strand displacement (TMSD) reaction. The system employs a detection probe that specifically binds to the target miRNA and sequentially releases a catalyst strand (CS) intended to trigger the subsequent TMSD reaction. Thus, the presence of target miRNA releases the CS that mediates the formation of an active G-quadruplex DNAzyme which is initially caged and inactivated by a blocker strand. In addition, a fuel strand that is supplemented for the recycling of the CS promotes another TMSD reaction, consequently generating a large number of active G-quadruplex DNAzymes. As a result, a distinct colorimetric signal is produced by the ABTS oxidation promoted by the peroxidase mimicking activity of the released G-quadruplex DNAzymes. Based on this novel strategy, we successfully detected miR-141, a promising biomarker for human prostate cancer, with high selectivity. The diagnostic capability of this system was also demonstrated by reliably determining target miR-141 in human serum, showing its great potential towards real clinical applications. Importantly, the proposed approach is composed of separate target recognition and signal transduction modules. Thus, it could be extended to analyze different target miRNAs by simply redesigning the detection probe while keeping the same signal transduction module as a universal signal amplification unit, which was successfully demonstrated by analyzing another target miRNA, let-7d.

Rapid and label-free fluorescence bioassay for microRNA based on exonuclease III-assisted cycle amplification

A new assay for the rapid and simple detection of microRNA based on G-quadruplex and Exonuclease III (ExoIII) dual signal amplification was constructed.