A T-rich nucleic acid-enhanced electrochemical platform based on electroactive silver nanoclusters for miRNA detection

Mesoporous Gold: Substrate-Dependent Growth Dynamics, Strain Accumulation, and Electrocatalytic Activity for Biosensing

Understanding the growth of mesoporous crystalline materials, such as mesoporous metals, on different substrates can provide valuable insights into the crystal growth dynamics and the redox reactions that influence their electrochemical sensing performance. Herein, it is demonstrated how the amorphous nature of the glass substrate can suppress the typical <111> oriented growth in mesoporous Au (mAu) films. The suppressed <111> growth is manifested as an accumulation of strain, leading to the generation of abundant surface defects, which are beneficial for enhancing the electrochemical activity. The fine structuring attained enables dramatically accelerated diffusion and enhances the electrochemical sensing performance for disease-specific biomolecules. As a proof-of-concept, the as-fabricated glass-grown mAu film demonstrates high sensitivity in electrochemical detection of SARS-CoV-2-specific RNA with a limit of detection (LoD) as low as 1 attomolar (aM).

Copper-cobalt dual-site on N-doped carbon nanotube with dual-promoted synergy for glucose electrochemical detection

Doping specific active sites and accelerating the decisive step of glucose catalysis to construct highly active glucose sensing electrochemical catalysts remains a major challenge for glucose sensing. Herein, we report the detailed design of Cu-Co dual active site N-doped carbon nanotube (CuCo-NCNTs) obtained by electrodeposition modification, programmed warming and calcination for electrochemical glucose detection. In the CuCo-NCNTs material system, Cu serves as the main active site for glucose sensing. Co with good adsorption of hydroxyl groups acts as the site providing hydroxyl groups to provide oxygen source for Cu oxidized glucose sensing. The synergistic effect between the two active sites in the Cu-Co system and the abundant micro-reactive sites exposed by carbon nanotubes greatly ensure the excellent electrocatalytic performance of glucose oxidation reaction. Therefore, CuCo-NCNTs have good electrocatalytic performance with a sensitivity of 0.84 mA mM-1 cm-2 and a detection limit of 1 μM, and also have excellent stability and specificity. DFT calculations elucidate the decisive steps of H-atom removal in the oxidation of glucose by Cu active site N-doped carbon nanotube (Cu-NCNTs) and Co active site N-doped carbon nanotube (CuCo-NCNTs) materials, illustrating the role of oxygen source provided by hydroxyl group adsorption in the electrochemical sensing process of glucose, thus demonstrating that the electrochemical sensing signal of glucose can be effectively enhanced when cobalt species that readily adsorb hydroxyl groups are introduced into the materials.

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.

Self-accelerated DNA walker mediated electrochemical biosensor for rapid and ultrasensitive detection of microRNA

Herein, we developed a novel three-dimensional (3D) self-accelerated DNA walker (SADW) which progressively expedite walking rate by unlocking the more walking arm continuously in walker process to construct electrochemical biosensor for ultrasensitive detection of microRNA. Particularly, we skillfully introduced a target analogue sequence in the double-loop hairpin, which could be released in the walking process of SADW, then rapidly activating more silenced walking strands to achieve the continuous self-acceleration, resulting in the expedited reaction rate. Surprisingly, the average reaction rate of SADW was quite higher than that of traditional 3D self-circulating DNA walkers (DW) under pretty low target miRNA concentration, which is ascribed to the outstanding acceleration process of the SADW, readily conquering the major predicaments of DW in detecting target with traces concentration: slow reaction rate and low sensitivity. This way, the elaborated SADW is favorably applied in the ultrasensitive and rapid detection of miRNA-21 in tumor cancer cell lysates with a detection limit down to 5.81 aM which was far from lower than the detection limit of DW. This approach develops the novel generation of widespread strategy for the applications in clinic diagnose, biosensing assay, and DNA nanobiotechnology.

miRNA Detection for Prostate Cancer Diagnosis by miRoll-Cas: miRNA Rolling Circle Transcription for CRISPR-Cas Assay

Micro-RNA (miRNA) emerges as a promising type of biomarker for cancer diagnosis. There is an urgent need for developing rapid, convenient, and precise miRNA detection methods that may be conducted with limited laboratory facilities, especially in underdeveloped areas. Herein, we developed a miRNA detection method termed miRoll-Cas, where miRNA is first amplified by rolling circle transcription and then subject to CRISPR-Cas13a assay. Using miRoll-Cas, we realized the sensitive detection of multiple cancer-relevant miRNA markers (miR21, miR141, and Let7b) and specifically identified other variants of the Let7 family, which can accurately discriminate prostate cancer patients from healthy people. We envision that miRoll-Cas may be readily translated to clinical applications in the diagnosis of a variety of diseases beyond cancer.

A sensitive electrochemical aptasensor for zearalenone detection based on target-triggered branched hybridization chain reaction and exonuclease I-assisted recycling

Traditional methods for detecting antibiotic and mycotoxin residues rely on large-scale instruments, which are expensive and require complex sample pretreatment processes and professional operators. Although aptamer-based electrochemical sensors have the advantages of simplicity, speed, low cost, and high sensitivity, most aptamer-based sensors lack a signal amplification strategy due to their direct use of aptamers as probes, resulting in insufficient sensitivity. To solve the sensitivity problem in the electrochemical detection process, a novel electrochemical sensing strategy was established for ultrasensitive zearalenone (ZEN) detection on the basis of exonuclease I (Exo I) and branched hybridization chain reaction (bHCR) to amplify the signal. The amplification strategy showed excellent analytical performance towards ZEN with a low detection limit at 3.1×10-12 mol/L and a wide linear range from 10-11 to 10-6 mol/L. Importantly, the assay was utilized in the corn powder samples with satisfactory results, holding promising applications in food safety detection and environmental monitoring.

Highly stable Ru-complex-based metal-covalent organic frameworks as novel type of electrochemiluminescence emitters for ultrasensitive biosensing

Developing novel types of high-performance electrochemiluminescence (ECL) emitters is of great significance for constructing ultrasensitive ECL sensors. Herein, a highly stable metal-covalent organic framework (MCOF), termed Ru-MCOF, has been devised and synthesized by employing a classic ECL luminophore, tris(4,4'-dicarboxylicacid-2,2'-bipyridyl)ruthenium(II) (Ru(dcbpy)₃²⁺), as building unit and applied as a novel ECL probe to construct an ultrasensitive ECL sensor for the first time. Impressively, the topologically ordered and porous architectures of the Ru-MCOF not only allow Ru(bpy)₃²⁺ units to precisely locate and homogeneously distribute in the skeleton via strong covalent bonds but also facilitate the transport of co-reactants and electrons/ions in channels to promote the electrochemical activation of both external and internal Ru(bpy)₃²⁺ units. All these features endow the Ru-MCOF with excellent ECL emission, high ECL efficiency, and outstanding chemical stability. As expected, the constructed ECL biosensor based on the Ru-MCOF as a high-efficiency ECL probe accomplishes the ultrasensitive detection of microRNA-155. Overall, the synthesized Ru-MCOF not only enriches the MCOF family but also displays excellent ECL performance and thus expands the application of MCOFs in bioassays. Considering the structural diversity and tailorability of MCOFs, this work opens a new horizon to design and synthesize high-performance ECL emitters, therefore paving a new way to develop highly stable and ultrasensitive ECL sensors and motivating further research on MCOFs.

Dual-sensitized heterojunction PDA/ZnO@MoS2 QDs combined with multilocus domino-like DNA cascade reaction for ultrasensitive photoelectrochemical biosensor

In this work, by integrating with a highly efficient multilocus domino-like cascade reaction on DNA nanonet, an ultrasensitive PEC biosensor based on dual-sensitized PDA/ZnO@MoS₂ QDs photoactive material as signal probe was proposed for detection of miRNA-182-5p. The dual-sensitized PDA/ZnO@MoS₂ QD composed by both of p-n and S-scheme heterojunctions on electrode generated an extremely high initial PEC signal, which however quenched by CdTe QDs decorated on DNA nanonet owing to the significant p-n quenching effect. Thereafter, the output DNA (RS) from DSN enzyme-assisted target recycling amplification triggered an ingenious multilocus domino-like DNA cascade reaction on DNA nanonet for releasing numerous CdTe QDs. Thanks to the multilocus domino-like mode that owned abundant binding sites for increasing trigger efficiency and drove cascade reaction automatically advance along four stated pathways, the target conversion rate could be improved effectively compared with that of traditional approaches, significantly enhancing the detection sensitivity. Consequently, the developed PEC biosensor exhibited a low detection limit to 0.17 fM, providing a new avenue for sensitive, fast and reliable sensing of various DNA/RNA.

Formation of miRNA Nanoprobes-Conjugation Approaches Leading to the Functionalization

Recently, microRNAs (miRNA) captured the interest as novel diagnostic and prognostic biomarkers, with their potential for early indication of numerous pathologies. Since miRNA is a short, non-coding RNA sequence, the sensitivity and selectivity of their detection remain a cornerstone of scientific research. As such, methods based on nanomaterials have emerged in hopes of developing fast and facile approaches. At the core of the detection method based on nanotechnology lie nanoprobes and other functionalized nanomaterials. Since miRNA sensing and detection are generally rooted in the capture of target miRNA with the complementary sequence of oligonucleotides, the sequence needs to be attached to the nanomaterial with a specific conjugation strategy. As each nanomaterial has its unique properties, and each conjugation approach presents its drawbacks and advantages, this review offers a condensed overview of the conjugation approaches in nanomaterial-based miRNA sensing. Starting with a brief recapitulation of specific properties and characteristics of nanomaterials that can be used as a substrate, the focus is then centered on covalent and non-covalent bonding chemistry, leading to the functionalization of the nanomaterials, which are the most commonly used in miRNA sensing methods.

Silver nano-reporter enables simple and ultrasensitive profiling of microRNAs on a nanoflower-like microelectrode array on glass

MicroRNAs (miRNAs) are small non-coding RNAs with ~ 22 nucleotides, playing important roles in the post-transcriptional regulation of gene expression. The expression profiles of many miRNAs are closely related to the occurrence and progression of cancer and can be used as biomarkers for cancer diagnosis and prognosis. However, their intrinsic properties, such as short length, low abundance and high sequence homology, represent great challenges in miRNA detection of clinical samples. To overcome these challenges, we developed a simple, ultrasensitive detection platform of electrochemical miRNAs chip (e-miRchip) with a novel signal amplification strategy using silver nanoparticle reporters (AgNRs) for multiplexed, direct, electronic profiling of miRNAs. A two-step hybridization strategy was used to detect miRNAs, where the target miRNA hybridizes with a stem-loop probe to unlock the probe first, and the opened stem-loop can further hybridize with AgNRs for signaling amplification. To enhance the detection sensitivity, the gold nanoflower electrodes (GNEs) were constructed in the microaperture arrays of the e-miRchips by electroplating. With the optimal size of the GNEs, the e-miRchip showed excellent performance for miR-21 detection with a detection limit of 0.56 fM and a linear range extended from 1 fM to 10 pM. The e-miRchip also exhibited good specificity in differentiating the 3-base mismatched sequences of the target miRNA. In addition, the e-miRchip was able to directly detect miR-21 expression in the total RNA extracts or cell lysates collected from lung cancer cells and normal cells. This work demonstrated the developed e-miRchip as an efficient and promising miniaturized point-of-care diagnostic device for the early diagnosis and prognosis of cancers.

Graphical Abstract

A pump-free and high-throughput microfluidic chip for highly sensitive SERS assay of gastric cancer-related circulating tumor DNA via a cascade signal amplification strategy

Circulating tumour DNA (ctDNA) has emerged as an ideal biomarker for the early diagnosis and prognosis of gastric cancer (GC). In this work, a pump-free, high-throughput microfluidic chip coupled with catalytic hairpin assembly (CHA) and hybridization chain reaction (HCR) as the signal cascade amplification strategy (CHA–HCR) was developed for surface-enhanced Raman scattering (SERS) assays of PIK3CA E542K and TP53 (two GC-related ctDNAs). The chip consisted of six parallel functional units, enabling the simultaneous analysis of multiple samples. The pump-free design and hydrophilic treatment with polyethylene glycol (PEG) realized the automatic flow of reaction solutions in microchannels, eliminating the dependence on external heavy-duty pumps and significantly improving portability. In the reaction region of the chip, products generated by target-triggered CHA initiated the HCR, forming long nicked double-stranded DNA (dsDNA) on the Au nanobowl (AuNB) array surface, to which numerous SERS probes (Raman reporters and hairpin DNA-modified Cu₂O octahedra) were attached. This CHA–HCR strategy generated numerous active “hot spots” around the Cu₂O octahedra and AuNB surface, significantly enhancing the SERS signal intensity. Using this chip, an ultralow limit of detection (LOD) for PIK3CA E542K (1.26 aM) and TP53 (2.04 aM) was achieved, and the whole process was completed within 13 min. Finally, a tumour-bearing mouse model was established, and ctDNA levels in mouse serum at different stages were determined. To verify the experimental accuracy, the gold-standard qRT–PCR assay was utilized, and the results showed a high degree of consistency. Thus, this rapid, sensitive and cost-effective SERS microfluidic chip has potential as an ideal detection platform for ctDNA monitoring.