DNA-templated silver nanoclusters locate microRNAs in the nuclei of gastric cancer cells

Artificial intelligence in theranostics of gastric cancer, a review

Gastric cancer (GC) is one of the commonest cancers with high morbidity and mortality in the world. How to realize precise diagnosis and therapy of GC owns great clinical requirement. In recent years, artificial intelligence (AI) has been actively explored to apply to early diagnosis and treatment and prognosis of gastric carcinoma. Herein, we review recent advance of AI in early screening, diagnosis, therapy and prognosis of stomach carcinoma. Especially AI combined with breath screening early GC system improved 97.4 % of early GC diagnosis ratio, AI model on stomach cancer diagnosis system of saliva biomarkers obtained an overall accuracy of 97.18 %, specificity of 97.44 %, and sensitivity of 96.88 %. We also discuss concept, issues, approaches and challenges of AI applied in stomach cancer. This review provides a comprehensive view and roadmap for readers working in this field, with the aim of pushing application of AI in theranostics of stomach cancer to increase the early discovery ratio and curative ratio of GC patients.

Detection of inflammatory bowel disease (IBD)-associated microRNAs by two color DNA-templated silver nanoclusters fluorescent probes

Researches demonstrated that circulating miRNAs could be used as novel diagnostic and prognostic potential markers for patients with inflammatory bowel diseases (IBD). It is of great significance in clinical to develop rapid and specific detection methods for miRNAs. Herein, we established a fluorescent probe for ulcerative colitis (UC) activity-associated two serum biomarkers (miR-23a and miR-223) simultaneous detection, which used multi-color fluorescent DNA-stabilized silver nanoclusters (DNA-AgNC) illuminated by a close guanine (G)-rich sequence as a signal transducer and two split DNA probes as recognition units. In principle, the two DNA probe sequences containing AgNC nucleation sequence and G-rich sequence respectively, formed a ternary complex when in the presence of target miRNA through base pairing, so as to induce enhancement of fluorescence emission of AgNC by shortening the distance from G-rich sequence. The combined probes for miR-23a and miR-223 detection generated increased fluorescence signals at 460 nm ex/545 nm em and at 560 nm ex/630 nm em, respectively. With this technique, we successfully quantified the two target miRNAs with high selectivity. Furthermore, the potential clinic applicability of this method was verified by testing the spiked standard miRNAs in human serum. Thus, this one-step, low-cost, and homogenous method offers a great opportunity for disease-associated multiplex miRNAs simultaneous detection.

Polyethyleneimine-protected silver cluster for label-free and highly selective detection of 2,4,6-trinitrotoluene

Sensitive and selective detection of 2,4,6-trinitrotoluene (TNT) is critical for environmental protection and public health. In this work, a convenient synthesis strategy for preparation of fluorescent PEI-AgNCs was described and further a facile and label-free sensing strategy for detection of TNT was developed. The hyperbranched polyethyleneimine (PEI) were used as template to one-step synthesize functional PEI-AgNCs with bright fluorescence signal and rich amino groups on their surface. PEI can specifically bind to electron-deficient TNT through donor-receptor interaction to form Meissenheimer complex. Interestingly, the absorption spectra of the Meissenheimer complex overlap with the fluorescence emission peak of PEI-AgNCs, thus quenching fluorescence of PEI-Ag NCs through fluorescence resonance energy transfer (FRET). Furthermore, this bonding process also initiate aggregation of PEI-AgNCs and quench the fluorescence of PEI-AgNCs by the aggregation-induced quenching (AIQ) effect. The novel method demonstrates sensitivity with a detection limit for TNT have been obtained as 17 nM. In addition, the proposed sensing method also has good selectivity over other potential interference and displayed a good potential application value in real water samples with satisfactory recoveries, offering a promising platform for sensing TNT in public safety and security environment protection.

DNA Templated Silver Nanoclusters for Bioanalytical Applications: A Review

Due to their unique programmability, biocompatibility, photostability and high fluorescent quantum yield, DNA templated silver nanoclusters (DNA Ag NCs) have attracted increasing attention for bioanalytical application. This review summarizes the recent developments in fluorescence properties of DNA templated Ag NCs, as well as their applications in bioanalysis. Finally, we herein discuss some current challenges in bioanalytical applications, to promote developments of DNA Ag NCs in biochemical analysis.

Long non-coding RNA terminal differentiation-induced non-coding RNA regulates cisplatin resistance of choroidal melanoma by positively modulating extracellular signal-regulated kinase 2 via sponging microRNA-19b-3p

In the present study, we aimed to investigate the role of long non-coding RNA terminal differentiation-induced non-coding RNA (TINCR) in cisplatin (DDP) resistance of choroidal melanoma (CM) and the potential molecular mechanisms. CM and non-CM tissues were collected from 60 CM patients. DDP-resistant CM cells were obtained by selection with linearly increased DDP treatment. The expression levels of TINCR, microR-19b-3p (miR-19b-3p), and extracellular signal-regulated kinase 2 (ERK-2) were detected by quantitative real-time PCR. Cholecystokinin octapeptide (CCK-8) assay was utilized to detect chemosensitivity and cell viability. Flow cytometry analysis was performed to detect apoptotic cells. The protein levels of Bax, Bcl-2, cleaved-caspase-3, ERK-2, and nuclear factor-kappa B p65 were measured by Western blot. RNA immunoprecipitation (RIP) and dual-luciferase reporter assays were performed to determine the relationship among TINCR, miR-19b-3p, and ERK-2. The results showed that the levels of TINCR and ERK-2 were markedly increased in DDP-resistant CM tissues and cells, while miR-19b-3p level was significantly reduced. TINCR knockdown reduced DDP resistance and cell viability and promoted cell apoptosis, while TINCR overexpression exhibited opposite effects. TINCR and ERK-2 were direct targets of miR-19b-3p. Further experiments revealed that TINCR enhanced DDP resistance in CM cells by regulating the miR-19b-3p/ERK-2/NF-kb axis. Taken together, our study revealed a critical role of TINCR in regulating DDP resistance in CM and suggested that TINCR is a potential cisplatin-resistant CM therapeutic target.

Inhibition of DNA replication initiation by silver nanoclusters

Silver nanoclusters (AgNCs) have outstanding physicochemical characteristics, including the ability to interact with proteins and DNA. Given the growing number of diagnostic and therapeutic applications of AgNCs, we evaluated the impact of AgNCs on DNA replication and DNA damage response in cell-free extracts prepared from unfertilized Xenopus laevis eggs. We find that, among a number of silver nanomaterials, AgNCs uniquely inhibited genomic DNA replication and abrogated the DNA replication checkpoint in cell-free extracts. AgNCs did not affect nuclear membrane or nucleosome assembly. AgNCs-supplemented extracts showed a strong defect in the loading of the mini chromosome maintenance (MCM) protein complex, the helicase that unwinds DNA ahead of replication forks. FLAG-AgNCs immunoprecipitation and mass spectrometry analysis of AgNCs associated proteins demonstrated direct interaction between MCM and AgNCs. Our studies indicate that AgNCs directly prevent the loading of MCM, blocking pre-replication complex (pre-RC) assembly and subsequent DNA replication initiation. Collectively, our findings broaden the scope of silver nanomaterials experimental applications, establishing AgNCs as a novel tool to study chromosomal DNA replication.

A novel disease-associated nucleic acid sensing platform based on split DNA-scaffolded sliver nanocluster

Disease-associated nucleic acids, such as DNAs and miRNAs, are important biomarkers for the diagnosis, prognosis and treatment guidance of human diseases. Therefore, the accurate and sensitive detection of nucleic acid is of great significance for the early diagnosis of diseases. DNA-scaffolded silver nanocluster (DNA-Ag NC) is a new type of probe with good photostability and low toxicity that has been widely used in biomedical analysis. In this work, a new universal sensing platform based on target triggered labeling luminescent DNA-Ag NC for disease-related nucleic acids detection was constructed. The assembled split DNA fragment pair (C₄AC₄T and C₃GT₄) could be used as a template to develop a bright green fluorescent Ag NC. According to this phenomenon, we devised two probe sequences DNA 1 and DNA 2, which could hybridize to the same one target and contained a different split fragment of Ag NC' scaffold. The target compelled the split fragments close to each other through base pairing with DNA 1 and DNA 2, thus quantification of the target could be achieved through measuring green fluorescence of Ag NC that produced by assembled scaffold in ternary hybrid products. We applied this platform successfully for miR-362, a potential biomarker of inflammatory bowel diseases (IBD), or HIV-related DNA (hDNA) detection, achieving the detection limits of 6.5 nM and 1.7 nM, respectively. Both of the assays showed excellent reproducibility, selectivity and potential applications in human serum samples. In summary, an economic and convenient universal platform was developed for disease-associated nucleic acid detection.

Nonenzyme Cascaded Amplification Biosensor Based on Effective Aggregation Luminescence Caused by Disintegration of Silver Nanoparticles

Sensitive and portable quantification of biomarkers has particular significance in the monitoring and treatment of clinical diseases. Conventional immunoassays were accustomed to introducing or incorporating enzymes for signal amplification, which commonly suffered from poor stability and inferior tolerance. Herein, we constructed a novel nonenzyme amplification methodology based on fluorogenic Ag⁺-tetrazolate aggregation coupled with silver corrosion sensitization for biomarker determination. A significant cascade enhancement strategy was achieved by the valid aggregation luminescence caused by the potent disintegration of silver nanoparticles. Furthermore, efficient magnetic separation was also combined and performed for the rapidity and simplicity of operation. As the target, the detection limit of prostate-specific antigen was 15.66 pg/mL in our designed biosensor. Besides, a good linear relationship was obtained. The designed biosensor demonstrated good specificity and was successfully applied to clinical serum sample detection.

Detection of microRNA using enzyme-assisted amplifying and DNA-templated silver nanoclusters signal-off fluorescence bioassay

A Simple and fast analysis strategy of fluorescence quenching based on DNA-templated silver nanoclusters was developed for detection of miR-122 related to diseases such as human liver. We used Exo III to cleave the silver cluster template and assist in the DNA-RNA complex cycle. When the target is absent, the silver cluster template remains intact, and DNA-AgNCs are generated under the action of AgNO₃/NaBH₄, producing a strong background fluorescence signal. Once the target is added, the site of the Exo III occurs after a series of hybridization cycles, the Exo III acts, the template DNA is continuously hydrolyzed, and the fluorescence intensity of the system is significantly reduced. By comparing the changes in the fluorescence signal, we found that this strategy has good sensitivity and the detection limit is as low as 84.0 pM. The strategy also has excellent discriminating ability and good selectivity, it can provide a persuasive reference for the early diagnosis of liver cancer and hepatitis.

Label-free probes using DNA-templated silver nanoclusters as versatile reporters

DNA-templated silver nanoclusters (DNA-AgNCs) have demonstrated pervasive applications in analytical chemistry recently. As a way of signal output in DNA-based detection methods, DNA-AgNCs have prominent advantages: first, the recognition and synthesizing sequences are naturally integrated in one DNA probe without any chemical modification or connection; second, the emissive wavelength of DNA-AgNCs can be adjusted in a wide range by employing different sequences; third, DNA-AgNCs can be utilized for producing not only fluorescence, also electrochemiluminescence and electrochemical signals. Besides, they also show potential applications for cell imaging, and are considered to be one of the most ideal nanomaterials for in-vivo imaging due to their ultra-small particle size. In this review, a brief and comprehensive introduction of DNA-AgNCs is firstly given, then label-free probes using DNA-AgNCs are classified and summarized, lastly concluding perspectives are provided on the defects and application potentials.

An aptamer-based fluorometric zearalenone assay using a lighting-up silver nanocluster probe and catalyzed by a hairpin assembly

An enzyme-free fluorometric assay is described for the determination of zearalenone (ZEN). The method combines (a) catalyzed hairpin assembly (CHA), (b) ultrahigh fluorescent light-up G-rich DNA sequences in proximity to silver nanoclusters (Ag NCs), and (c) the use of aptamers (Apt). In the presence of ZEN, the inhibit sequence (Inh) is released from the aptamer-trigger sequence (Apt-T) via the binding of ZEN and the aptamer of Apt-T. The free Apt-T acts as a switch that opens the hairpins H1 and H2 to generate H1-H2 complex. The released Apt-T is available to trigger the next round of CHA between H1 and H2. Finally, the hybridization between H1 and the Ag NCs probe (P) causes the G-rich sequence to be in close proximity to the dark Ag NCs encapsulated by P. This leads to highly efficient lighting up of the Ag NCs and the production of amplified fluorescence with excitation/emission peaks at 575/628 nm. Under the optimized conditions, a linear correlation was observed with concentrations ranging from 1.3 pg mL^-1 to 100 ng mL^-1, and the limit of detection was 0.32 pg mL^-1 (at S/N = 3). The method was successfully validated by analyzing maize and beer for levels of ZEN after a simple sample preparation procedure. Graphical abstractSchematic of the assay. The inhibit sequence (Inh) is released from aptamer-trigger sequence (Apt-T) via binding of ZEN and aptamer. The free Apt-T triggers catalyzed hairpin assembly (CHA).G-rich DNA is in proximity to silver nanoclusters (Ag NCs) and fluorescence intensity increases to detect ZEN.

Plasmon Coupling-Enhanced Raman Sensing Platform Integrated with Exonuclease-Assisted Target Recycling Amplification for Ultrasensitive and Selective Detection of microRNA-21

A "signal-off" surface-enhanced Raman scattering (SERS) platform has been constructed for ultrasensitive detection of miRNA-21 by integrating exonuclease-assisted target recycling amplification with a plasmon coupling enhancement effect. On this platform, Raman-labeled Au nanostar (AuNS) probes can be covalently linked with the thiolated aptamer (Apt) on the Au-decorated silicon nanowire arrays (SiNWAs/Au) substrate, creating a coupled electromagnetic field between the substrate and the probes to enhance Raman signal. In the presence of miRNA-21, T7 exonuclease specifically hydrolyzed Apt on Apt/miRNA duplex to release miRNA-21. The regenerated element could then initiate another cycle of Apt/miRNA duplex formation and Apt cleavage. Correspondingly, the capture ability of substrate toward probes and the plasmon coupling effect between them were both diminished, giving a prominent attenuation of Raman intensity that can work as the detection signal. Due to the cascading integration between the target cycle process and the plasmon coupling effect, the present platform displayed a very low detection limit (0.34 fM, 3σ) for miRNA-21 detection. Furthermore, it was proven to be effective for analyzing miRNA-21 in biological samples and distinguishing the expression levels of miRNA-21 in MCF-7 cells and NIH3T3 cells, which became a promising tool to monitor miRNA-21 in cancer auxiliary diagnosis and drug screening.

Polydopamine nanosphere@silver nanoclusters for fluorescence detection of multiplex tumor markers

There is an increasing demand to establish a convenient and stable analytical methodology for screening multiplex tumor markers in early diagnosis of cancers. In this work, an innovative fluorescence method is proposed for simultaneous detection of alpha-fetoprotein (AFP) and carcinoembryonic antigen (CEA). A polydopamine nanosphere@silver nanocluster (PDAN@AgNC) system is introduced for fluorescence quenching and recovery. The AgNCs with different emissions are synthesized using different DNA templates, which also contain aptamer sequences towards AFP and CEA, respectively. These single-stranded DNA sequences could be adsorbed on the surface of the PDAN through π-π stacking, which results in the quenching of AgNCs. However, in the presence of the corresponding tumor marker, the aptamer/target complex forms which releases AgNCs from the surface of the PDAN and the recovered fluorescence could be used to indicate the concentration of the tumor marker. This PDAN@AgNC system has been validated preliminarily to screen human serum samples with excellent results. Taking advantages of simplicity, enzyme/antibody-free nature, low cost and convenient operation, the proposed biosensor has great potential to be used in biomedical research studies and clinical diagnosis.

Novel Fluorescence Switch for MicroRNA Imaging in Living Cells Based on DNAzyme Amplification Strategy

MicroRNAs (miRNAs) play important roles in the regulation of target gene expression and cell development. Therefore, developing of accurate and visual detection methods for miRNAs is important for early diagnosis of cancer. In this study, we established a visual detection method for miRNA 155 based on DNAzyme amplification strategy in living cells. MnO₂ nanosheets were employed to deliver locked DNAzyme and substrate DNA into cells. The gold nanoparticle (AuNP) probe was taken up by cells autonomously. Then, MnO₂ nanosheets were reduced to Mn²⁺ by glutathione in cells and DNA modules were released. MiRNA 155 took away locker DNA by strand displacement reaction to activate the DNAzyme. Then, the DNAzyme cleaved the substrate DNA and released single-stranded DNA named key DNA. Then, Key DNA hybridized with the hairpin DNA, making cy5 far away from AuNP and turning on its fluorescence. One target miRNA led to plenty of released key DNA when lots of substrate DNA was added. Thus, the visual detection of miRNA 155 in living cells would be initiated. Under confocal laser microscopy, the fluorescence was obviously observed in tumor cells but not in normal cells. The method has a linear range from 0.1 to 10 nM and a low detection limit of 44 pM on in vitro detection.