Electrophoretic mobility shift as a molecular beacon-based readout for miRNA detection

An Au-Se bond-based fluorescent nanoprobe for thermophoretic aggregation imaging of exosomal miRNAs

Exosomal microRNAs (miRNAs) have recently gained prominence as promising biomarkers for non-invasive lung cancer screening. In this study, we innovatively developed an innovative fluorescent nanoprobe based on stable Au-Se bonds to detect lung cancer-associated miRNAs in exosomes. This nanoprobe integrates gold nanoparticles with selenated DNA molecular beacons (MBs) conjugated via 1,4-phenyldiisothiocyanate (PDITC). It demonstrates exceptional stability in high-thiol environments, making it ideal for high-fidelity imaging and biomarker detection in biological settings. By integrating molecular beacons that specifically recognize and bind to target exosomal miRNAs, the nanoprobe enables precise detection. Thermophoretic aggregation imaging of exosomes was achieved using confocal fluorescence microscopy with 1064 nm laser irradiation. Our findings demonstrate that this nanoprobe efficiently identifies lung cancer-related miRNAs in exosomes, providing a promising candidate for early lung cancer detection in clinical applications.

Nanopore-based detection of periodontitis biomarker miR31 in saliva samples

MicroRNAs (miRNAs) play important roles in posttranscriptional gene regulation. Aberrations in the miRNA levels have been the cause behind various diseases, including periodontitis. Therefore, sensitive, specific, and accurate detection of disease-associated miRNAs is vital to early diagnosis and can facilitate inhibitor screening and drug design. In this study, we developed a label-free, real-time sensing method for the detection of miR31, which has been frequently linked to periodontitis, using an engineered protein nanopore and in the presence of a complementary ssDNA as a molecular probe. Our method is rapid and highly sensitive with nanomolar concentration of miR31 that could be determined in minutes. Furthermore, our sensor showed high selectivity toward the target miR31 sequence even in the presence of interfering nucleic acids. In addition, artificial saliva and human saliva samples were successfully analyzed. Our developed nanopore sensing platform could be used to detect other miRNAs and offers a potential application for the clinical diagnosis of disease biomarkers.

Evaluation of miR-155 silencing using a molecular beacon in human lung adenocarcinoma cell line

Lung cancer (LC) is a leading cause of global cancer-related deaths, highlighting the development of innovative methods for biomarker detection improving the early diagnostics. microRNAs (miRs) alterations are known to be involved in the initiation and progression of human cancers and can act as biomarkers for diagnostics and treatment. Herein, we develop the application of molecular beacon (MB) technology to monitor miR-155-3p expression in human lung adenocarcinoma A549 cells without complementary DNA synthesis, amplification, or expensive reagents. Furthermore, we produced gold nanoparticles (AuNPs) for delivering antisense oligonucleotides into A549 cells to reduce miR-155-3p expression, which was subsequently detectable using the MB. The MB was designed and structural characterized by Förster Resonance Energy Transfer (FRET)-melting, Circular Dichroism (CD), Nuclear magnetic resonance (NMR), and fluorometric experiments, and then the hybridization conditions were optimized for an in vitro approach involving the detection of miR-155-3p in total RNA extracted from A549 cell line. The expression profile of miR-155-3p was obtained by RT-qPCR. The results demonstrated that MB was properly designed and showed efficacy in targeting miR-155-3p. Furthermore, a limit of detection down to nanomolar concentration was achieved and the specificity of the biosensor was proved. Moreover, the self-assembly of ASOs with AuNPs exhibited exceptional target specificity, effectively silencing miR-155-3p. Notably, compared to lipid-based transfection agent, AuNPs displayed superior silencing efficiency. We highlighted the ability of MB to detect changes in the target gene expression after gene silencing. Overall, this innovative approach represents a promising tool for detecting various biomarkers at the same time, with potential applications in clinical settings.

Self-assembly of hyperbranched DNA network structure for signal amplification detection of miRNA

Catalytic hairpin assembly (CHA) and hybridization chain reaction (HCR) can achieve the high sensitivity and rapid reaction rate in detecting miRNA. However, the amplification efficiency by these methods are limited. Herein, an enzyme-free and label-free hyperbranched DNA network structure (HDNS) was designed, in which localized catalytic hairpin assembly (LCHA) and hybridization chain reaction occurred in the horizontal axis and longitudinal axis, respectively, exhibiting intensive signal dual-amplification. miRNA-122 was selected as the target on behalf of miRNA to design the HDNS sensor. The fluorescence signal change of HDNS showed good linearity for detecting miRNA-122 in the concentration range from 0.1 nM to 60 nM with a limit of detection (LOD) at 37 pM which was lower than those of the sensors based on separate CHA or HCR. Afterwards, the HDNS sensor was applied to detect miRNA-122 in serum samples with the recovery rate in the range of 97.2 %-107 %. The sensor could distinguish different kinds of miRNAs, even the family members with high sequence homology, exhibiting excellent selectivity. This method provided a novel design strategy for improving the sensitivity and selectivity of DNA sensor for miRNA detection.

Ultrasensitive and Visual Electrochemiluminescence Ratiometry Based on a Constant Resistor-Integrated Bipolar Electrode for MicroRNA Detection

In this work, a new electrochemiluminescence (ECL) platform was constructed for detecting the prostate cancer marker microRNA-141 (miRNA-141) on a constant resistor-integrated closed bipolar electrode (BPE). It consisted of two reservoirs and a constant resistor, and both ends were connected to the anode of the driving electrode and the cathode of BPE. The cathode of BPE was modified with boron nitride quantum dots (BNQDs), and the anode reservoir was the [Ru(bpy)₃](PF₆)₂/TPrA system. After introducing a certain amount of hairpin DNA 3 (H3) and ferrocene-labeled single-stranded DNA (Fc-ssDNA) on the surface of the BNQDs, the ECL emission signal of the BNQDs was difficult to be observed by the naked eye, while [Ru(bpy)₃](PF₆)₂ emitted a strong and visible ECL signal. In the presence of the target, bipedal DNA assembled by catalytic hairpin assembly (CHA) took away the Fc-ssDNA and the ECL intensity of the BNQDs was enlarged, and as the concentration of miRNA-141 increased to the cutoff value, yellow-green light was visible by the naked eye. Meanwhile, the red emission signal of [Ru(bpy)₃](PF₆)₂/TPrA became weakened. Thus, an ultrasensitive "color switch" ECL biosensor for detection of miRNA-141 was constructed and endowed with a wide linear range from 10^-17 to 10^-7 M and a detection limit of 10^-17 M (S/N = 3). This study provides the potential for investigating portable devices in the detection of low-concentration nucleic acids.

A facile biosynthesis strategy of plasmid DNA-derived nanowires for readable microRNA logic operations

Multiple microRNAs (miRNAs) logical assays have attracted wide attention recently, which can be applied to mimic and reveal cellular events at the molecular level. However, it remains challenging to develop...