Catalytic hairpin self-assembly regulated chameleon silver nanoclusters for the ratiometric detection of CircRNA

CRISPR/Cas12a-derived ratiometric fluorescence sensor for high-sensitive Pb2+ detection based on CDs@ZIF-8 and DNAzyme

Benefiting from specific target recognition and trans-cleavage capabilities, the CRISPR/Cas12a system has great application prospects in the design of highly sensitive and rapid fluorescence biosensors. The CRISPR/Cas12a-based fluorophore-quencher molecular beacons exhibit single-color emission and are easily exposed to interference from environmental factors. Herein, we design a CRISPR/Cas12a-derived ratiometric fluorescence sensor for Pb2+ detection based on embedded carbon dots@zeolitic imidazolate framework-8 (CDs@ZIF-8) composites and DNAzyme. The functions of ZIF-8 about encapsulating red emissive CDs in the inner cavity and adsorbing DNA on the outer surface are integrated to establish dual fluorescence signals, thereby reducing the possibility of interference and improving sensing accuracy. The presence of Pb2+ is converted into the change of activator by the GR5 DNAzyme to activate the CRISPR/Cas12a system, which provides signal amplification through multiple turnovers of side branch cutting, achieving highly sensitive detection of Pb2+ with a low detection limit of 18 pM. This method has the advantages of simplicity, universality, and excellent quantitative ability, and has broad prospects in sensing applications.

Optical Nanobiosensor Based on Surface-Enhanced Raman Spectroscopy and Catalytic Hairpin Assembly for Early-Stage Lung Cancer Detection via Blood Circular RNA

Lung cancer has become the leading cause of cancer-related deaths globally. However, early detection of lung cancer remains challenging, resulting in poor outcomes for the patients. Herein, we developed an optical biosensor integrating surface-enhanced Raman spectroscopy (SERS) with a catalyzed hairpin assembly (CHA) to detect circular RNA (circRNA) associated with tumor formation and progression (circSATB2). The signals of the Raman reporter were considerably enhanced by generating abundant SERS "hot spots" with a core-shell nanoprobe and 2D SERS substrate with calibration capabilities. This approach enabled the sensitive (limit of detection: 0.766 fM) and reliable quantitative detection of the target circRNA. Further, we used the developed biosensor to detect the circRNA in human serum samples, revealing that patients with lung cancer had higher circRNA concentrations than healthy subjects. Moreover, we characterized the unique circRNA concentration profiles of the early stages (IA and IB) and subtypes (IA1, IA2, and IA3) of lung cancer. These results demonstrate the potential of the proposed optical sensing nanoplatform as a liquid biopsy and prognostic tool for the early screening of lung cancer.

Ratiometric fluorescence immunoassay based on silver nanoclusters and calcein-Ce3+ for detecting ochratoxin A

Ochratoxin A (OTA), a dangerous mycotoxin, is found in many crops. It is essential to create sensitive OTA detection techniques to ensure food safety. Based on the principle of p-nitrophenol (PNP) quenched the fluorescence of bovine serum albumin silver nanocluster (BSA-AgNCs) through an internal filtering effect, and phosphate activated fluorescence of calcein-Ce3+ system, a ratiometric fluorescence immunoassay for OTA detection was developed. In this strategy, the value of F518/F640 was used as a signal for response of OTA concentration. The detection range of this strategy was 0.625-25 ng/mL, the limit of detection (LOD) was 0.04 ng/mL. This new immunoassay offered a brand-new platform for detecting OTA.

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.

A DNA octahedral amplifier for endogenous circRNA detection and bioimaging in living cells and its biomarker study

The discovery of reliable biomarkers is essential for early diagnosis, treatment, and prognosis assessment of diseases. Many research studies have shown that circRNA is a potential biomarker for diagnosis and prognosis of diseases. However, in situ monitoring circRNA in live cells is still a challenge at present, which brings a major limitation to the development and verification of circRNA as a disease biomarker. In this study, a catalytic hairpin assembly (CHA) reaction-based DNA octahedral amplifier (DOA) was developed for fluorescence resonance energy transfer (FRET) detection and bioimaging of circRNA in living cells. The DOA was first produced by self-assembling a DNA octahedron with six customized single-stranded DNAs, and two hairpins H1 (Cy3) and H2 (Cy5) were then hybridized to four vertices of the DNA octahedron. Idiopathic pulmonary fibrosis (IPF)-related circHIPK3 was used as the target. Once the CHA reaction from H1 and H2 on DOA was activated by a sequence-specific back-splice junction (BSJ) of circHIPK3, a significant FRET signal can be obtained from Cy3 to Cy5. The circHIPK3 was subsequently released to cause the next CHA reaction. Because the DOA has the advantages of the spatial-confinement effect, resistance to nuclease degradation and easy penetration into cells, rapid and excellent signal amplification FRET detection and bioimaging of endogenous circHIPK3 can be achieved in various cells. This study provides a high-precision assay platform to explore the possibility of using circRNA as a biomarker, and it is valuable for circRNA-related early diagnosis and treatment of diseases.

Construction of Fluorescent G-Quadruplex Nanowires for Label-Free and Accurate Monitoring of Circular RNAs in Breast Cancer Cells and Tissues with Low Background

Circular RNAs (circRNAs) represent an emerging category of endogenous transcripts characterized by long half-life time, covalently closed structures, and cell-/tissue-specific expression patterns, making them potential disease biomarkers. Herein, we demonstrate the construction of fluorescent G-quadruplex nanowires for label-free and accurate monitoring of circular RNAs in breast cancer cells and tissues by integrating proximity ligation-rolling circle amplification cascade with lighting up G-quadruplex. The presence of target circRNA facilitates the SplintR ligase-mediated ligation of the padlock probe. Upon the addition of primers, the ligated padlock probe can serve as a template to initiate subsequent rolling circle amplification (RCA), generating numerous long G-quadruplex nanowires that can incorporate with thioflavin T (ThT) to generate a remarkably improved fluorescence signal. Benefiting from good specificity of SplintR ligase-mediated ligation reaction and exponential amplification efficiency of RCA, this strategy can sensitively detect target circRNA with a limit of detection of 4.65 × 10-18 M. Furthermore, this method can accurately measure cellular circRNA expression with single-cell sensitivity and discriminate the circRNA expression between healthy para-carcinoma tissues and breast cancer tissues, holding great potential in studying the pathological roles of circRNA and clinic diagnostics.

Alkaline phosphatase triggered gold nanoclusters turn-on fluorescence immunoassay for detection of Ochratoxin A

Ochratoxin A (OTA) is a highly toxic mycotoxin which can cause a variety of diseases. Sensitive detection of OTA is significant for food safety. Herein, a feasible and sensitive immunoassay was established for OTA detection by alkaline phosphatase (ALP) triggered gold nanoclusters (AuNCs) turn-on fluorescence. The fluorescence of the AuNCs can be quenched by Cr6+ induced aggregation of AuNCs and the fluorescence resonance energy transfer (FRET) between AuNCs and Cr6+. Under the catalytic action of ALP-labelled IgG (IgG-ALP), the ascorbic acid 2-phosphate (AA2P) was hydrolyzed to ascorbic acid (AA) for the reducing of Cr6+ to Cr3+. As a result, the degrees of AuNCs aggregation and FRET were weakened and the fluorescence of AuNCs was turned on. The amount of OTA in the sample was negatively correlated with the amount of IgG-ALP captured by anti-OTA monoclonal antibody (McAb) in the microplate. In optimal conditions, the turn-on fluorescence immunoassay had a good linear range of 6.25-100 ng/mL, and the detection limit was 0.693 ng/mL. The recoveries of OTA from corn were 95.89%-101.08% for the fluorescence immunoassay. This work provided a feasible, sensitive and good selectivity fluorescence method for OTA detection.

Application of microfluidic technology based on surface-enhanced Raman scattering in cancer biomarker detection: A review

With the continuous discovery and research of predictive cancer-related biomarkers, liquid biopsy shows great potential in cancer diagnosis. Surface-enhanced Raman scattering (SERS) and microfluidic technology have received much attention among the various cancer biomarker detection methods. The former has ultrahigh detection sensitivity and can provide a unique fingerprint. In contrast, the latter has the characteristics of miniaturization and integration, which can realize accurate control of the detection samples and high-throughput detection through design. Both have the potential for point-of-care testing (POCT), and their combination (lab-on-a-chip SERS (LoC-SERS)) shows good compatibility. In this paper, the basic situation of circulating proteins, circulating tumor cells, exosomes, circulating tumor DNA (ctDNA), and microRNA (miRNA) in the diagnosis of various cancers is reviewed, and the detection research of these biomarkers by the LoC-SERS platform in recent years is described in detail. At the same time, the challenges and future development of the platform are discussed at the end of the review. Summarizing the current technology is expected to provide a reference for scholars engaged in related work and interested in this field.

Asymmetric Hairpins DNA Encapsulated Silver Nanoclusters for In Situ Fluorescence Imaging of Fusion Gene Isoforms in Bone Marrow

Rapid and accurate imaging of the BCR/ABL fusion gene isoforms (e.g., e13a2, e14a2 and co-expression type) of chronic myeloid leukemia (CML) is of vital importance to first-line drug selection, but there is no assay that meets clinical needs (e.g., clinical kits > 18 h without isoforms information). Herein, an in situ imaging platform is developed for the rapid and accurate detection of CML fusion gene isoforms using asymmetric sequence-enhanced hairpins DNA encapsulated silver nanoclusters (ADHA) and catalyzed hairpin assembly (CHA). The specific detection of e13a2 and e14a2 fusion gene isoforms with detection limits of 19.2 am (11.558 copies µL-1 ) and 32.56 am (19.601 copies µL-1 ) in one-pot is achieved. The feasibility of the developed assay for real-world applications are demonstrated by one-step fluorescence imaging (40 min) of e13a2, e14a2 and co-expression type in bone marrow quantitatively (International Standard: 15.66%-168.878%) and further validated by cDNA-sequencing. This work suggests that the developed imaging platform holds great potential for rapid identification of the fusion gene isoforms and isoform related treatment monitoring.

Dual-channel fluorescence detection of antibiotic resistance genes based on DNA-templated silver nanoclusters

The aqueous environment is an ideal site for the generation and transmission of antibiotic resistance genes (ARGs), and has become a sink for multiple ARGs. Detection of multiple ARGs in one-pot by a simple method is essential to control the spread of antibiotic resistance. Herein, we developed a novel fluorescence sensing strategy based on chameleon DNA-templated silver nanoclusters (AgNCs) to achieve simultaneous detection of two ARGs (tet-A and sul-1). A DNA fluorescent probe with AgNCs stabilized at both termini and another DNA probe carried enhancer sequences were designed. The hybridization of the target ARGs and probes can form an infinitely extended linear DNA structure containing multi-branched AgNCs beacons, and the chameleon AgNCs approach the fluorescence enhancer sequence, thereby realizing the transduction and amplification of green and red fluorescence signals. Through this strategy, we successfully achieved highly specific detection of two ARGs with the LOD of 0.45 nM for tet-A and 0.32 nM for sul-1. In addition, the strategy still had good applicability in the detection of actual samples containing complex components. In this study, fluorescent DNA-AgNCs were applied to the rapid, enzyme-free and reliable detection of ARGs for the first time. The excellent performance of the simultaneous detection of two ARGs displayed that this method can be used to simultaneously analyze different types of ARGs, indicating its great potential in rapid screening and quantitative detection of ARGs in various environmental medias.

Docking-aided rational tailoring of a fluorescence- and affinity-enhancing aptamer for a label-free ratiometric malachite green point-of-care aptasensor

Although nucleic acid aptasensors are increasingly applied in the detection of environmentally hazardous biomolecules, several formidable challenges remain with this technique because of their vulnerability, high cost and suboptimal sensitivity. Here, a docking-aided rational tailoring (DART) strategy was established at three levels and in two dimensions for the refinement of malachite green (MG) DNA aptamers. Guided by in silico molecular docking, coarse and fine tailoring were conducted at three levels each, to significantly enhance fluorescence activation intensity and binding affinity in two dimensions. Empowered by the results of the rational tailoring, a mechanistic view of the MG DNA aptamer-target interaction was thoroughly analyzed via four types of interactions. To meet the demand for point-of-care testing (POCT), a label-free and ratiometric fluorescent aptasensor was developed leveraging the tailored MG aptamer, based on the binding site competition-equilibrium effect via the introduction of a reference dye. This sensitive, specific, low-cost and rapid aptasensor subsequently demonstrated outstanding detection performance, achieving an ideal signal response range of 5 nmol·L^-1 - 6 μmol·L^-1 and a low limit of detection (LOD) of 1.49 nmol·L^-1. The DART strategy and systematic exploration of the MG DNA luminescent aptamers herein will provide a valuable reference in the field of aptamer tailoring, biosensing and bioimaging. The proposed label-free ratiometric aptasensor also provides a highly generalizable strategy for hazardous biomolecular detection.

Programmable Nanostructures Based on Framework-DNA for Applications in Biosensing

DNA has been actively utilized as bricks to construct exquisite nanostructures due to their unparalleled programmability. Particularly, nanostructures based on framework DNA (F-DNA) with controllable size, tailorable functionality, and precise addressability hold excellent promise for molecular biology studies and versatile tools for biosensor applications. In this review, we provide an overview of the current development of F-DNA-enabled biosensors. Firstly, we summarize the design and working principle of F-DNA-based nanodevices. Then, recent advances in their use in different kinds of target sensing with effectiveness have been exhibited. Finally, we envision potential perspectives on the future opportunities and challenges of biosensing platforms.

Clinical application and detection techniques of liquid biopsy in gastric cancer

Gastric cancer (GC) is one of the most common tumors worldwide and the leading cause of tumor-related mortality. Endoscopy and serological tumor marker testing are currently the main methods of GC screening, and treatment relies on surgical resection or chemotherapy. However, traditional examination and treatment methods are more harmful to patients and less sensitive and accurate. A minimally invasive method to respond to GC early screening, prognosis monitoring, treatment efficacy, and drug resistance situations is urgently needed. As a result, liquid biopsy techniques have received much attention in the clinical application of GC. The non-invasive liquid biopsy technique requires fewer samples, is reproducible, and can guide individualized patient treatment by monitoring patients' molecular-level changes in real-time. In this review, we introduced the clinical applications of circulating tumor cells, circulating free DNA, circulating tumor DNA, non-coding RNAs, exosomes, and proteins, which are the primary markers in liquid biopsy technology in GC. We also discuss the current limitations and future trends of liquid biopsy technology as applied to early clinical biopsy technology.

Non-coding RNAs regulate the BMP/Smad pathway during osteogenic differentiation of stem cells

MicroRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs) are involved in the regulation of bone metabolism. The BMP/Smad pathway is a key signaling pathway for classical regulation of osteogenic differentiation. Non-coding RNAs (ncRNAs) and the BMP/Smad pathway both have important roles for osteogenic differentiation of stem cells, bone regeneration, and development of bone diseases. There is increasing evidence that ncRNAs interact with the BMP/Smad pathway to regulate not only osteogenic differentiation of stem cells but also progression of bone diseases, such as osteoporosis (OP), myeloma, and osteonecrosis of the femoral head (ONFH), by controlling the expression of bone disease-related genes. Therefore, ncRNAs that interact with BMP/Smad pathway molecules are potential targets for bone regeneration as well as bone disease diagnosis, prevention, and treatment. However, despite extensive studies on ncRNAs associated with the BMP/Smad pathway and osteogenic differentiation of stem cells, there is a lack of comparability. Moreover, some bone disease-associated ncRNAs with low abundance can be difficult to detect and there is a lack of mature delivery systems for their stable translocation to target sites, thus limiting their application. In this review, we summarize the research progress on interactions between ncRNAs and the BMP/Smad pathway during osteogenic differentiation of various stem cells and in the regulation of bone regeneration and bone diseases.

A SERS Biosensor Based on Functionalized Au-SiNCA Integrated with a Dual Signal Amplification Strategy for Sensitive Detection of Telomerase Activity During EMT in Laryngeal Carcinoma

Purpose

This paper aims to construct a surface-enhanced Raman spectroscopy (SERS) biosensor based on functionalized Au-Si nanocone arrays (Au-SiNCA) using a dual signal amplification strategy (SDA-CHA) to evaluate telomerase activity during epithelial-mesenchymal transition (EMT) in laryngeal carcinoma (LC).

Methods

A SERS biosensor based on functionalized Au-SiNCA was designed with an integrated dual-signal amplification strategy to achieve ultrasensitive detection of telomerase activity during EMT in LC patients.

Results

Labeled probes (Au-AgNRs@4-MBA@H₁) and capture substrates (Au-SiNCA@H₂) were prepared by modifying hairpin DNA and Raman signal molecules. Using this scheme, telomerase activity in peripheral mononuclear cells (PMNC) could be successfully detected with a limit of detection (LOD) as low as 10^-6 IU/mL. In addition, biological experiments using BLM treatment of TU686 effectively mimicked the EMT process. The results of this scheme were highly consistent with the ELISA scheme, confirming its accuracy.

Conclusion

This scheme provides a reproducible, selective, and ultrasensitive assay for telomerase activity, which is expected to be a potential tool for the early screening of LC in future clinical applications.