Recent advance of RNA aptamers and DNAzymes for MicroRNA detection

Color-Coded Traffic Signal Method Combined with Nanodiamond Quantum Sensing for Accurate miRNA Detection

Background noise interferes with the accurate detection of early tumor biomarkers. This study introduces a method that effectively reduces background noise to enhance detection accuracy by combining a color-coded signaling approach with the unique fluorescent properties and room-temperature tunable quantum spin characteristics of fluorescent diamonds (FNDs) with nitrogen-vacancy centers. In this approach, a red signal indicates the presence of the target analyte within the spectral region, a green signal indicates its absence, and a yellow signal indicates the need for further analysis using FNDs' quantum spin properties for optical detection magnetic resonance (ODMR) to distinguish the FND signal from background noise. Preliminary results demonstrate that this method enables the detection of breast cancer-related miRNA-21 and miRNA-96 concentrations as low as 1 fM within a 100 × 100 μm2 area, achieving single-molecule detection capability. This method is suitable for accurate biomarker identification and detection under high-background fluorescence conditions.

A two-color fluorescence sensing strategy based on functionalized tetrahedral DNAzyme nanotweezers for ochratoxin A detection

A two-color fluorescent sensing strategy based on a functionalized tetrahedral DNAzyme nanotweezer (FTDN) was developed to detect ochratoxin A (OTA) utilizing the multifunctional properties of DNA nanotechnology. The FTDN enables rapid OTA detection directly through a Cy5 fluorescent group, modified to respond to the target signal. Additionally, FTDN exhibits DNAzyme cutting activity in the presence of Mg2⁺ ions, enabling it to traverse DNA nanoflower-functionalized magnetic beads. This process results in the continuous cleavage of DNA nanoflowers labeled with numerous FAM fluorescent groups, thereby amplifying the detection signal and enhancing OTA sensitivity. The linear ranges for the Cy5 and FAM signals in response to OTA were 5-1000 ng/mL and 0.05-100 ng/mL, respectively, with corresponding limits of detection (LOD) of 1.59 ng/mL and 0.03 ng/mL. This study demonstrates that dual-color fluorescence via Cy5 and FAM can effectively verify OTA detection in food, significantly reducing false-positive and false-negative rates. The proposed platform offers sensitive and accurate detection of mycotoxins in food and can be adapted for monitoring other trace contaminants by simply altering the aptamer.

Recent Advances in DNA-Based Nanoprobes for In vivo MiRNA Imaging

As a post transcriptional regulator of gene expression, microRNAs (miRNA) is closely related to many major human diseases, especially cancer. Therefore, its precise detection is very important for disease diagnosis and treatment. With the advancement of fluorescent dye and imaging technology, the focus has shifted from in vitro miRNA detection to in vivo miRNA imaging. This concept review summarizes signal amplification strategies including DNAzyme catalytic reaction, hybrid chain reaction (HCR), catalytic hairpin assembly (CHA) to enhance detection signal of lowly expressed miRNAs; external stimuli of ultraviolet (UV) light or near-infrared region (NIR) light, and internal stimuli such as adenosine triphosphate (ATP), glutathione (GSH), protease and cell membrane protein to prevent nonspecific activation for the avoidance of false positive signal; and the development of fluorescent probes with emission in NIR for in vivo miRNA imaging; as well as rare earth nanoparticle based the second near-infrared window (NIR-II) nanoprobes with excellent tissue penetration and depth for in vivo miRNA imaging. The concept review also indicated current challenges for in vivo miRNA imaging including the dynamic monitoring of miRNA expression change and simultaneous in vivo imaging of multiple miRNAs.

A novel dual-mode aptasensor based on a multiple amplification system for ultrasensitive detection of lead ions using fluorescence and surface-enhanced Raman spectroscopy

In this work, we develop a dual recycling amplification aptasensor for sensitive and rapid detection of lead ions (Pb2+) using fluorescence and surface-enhanced Raman scattering (FL-SERS). The aptasensor allows targeted cleavage of substrates through specifically binding with the Pb2+-dependent aptamer (M-PS2.M). Ultrasensitive detection of trace Pb2+ has been achieved using an enzyme-free nonlinear hybridization chain reaction (HCR) and the FL-SERS technique. The lower limit of detection (LOD = 3σ/k) is 0.115 pM in FL mode and 1.261 fM in SERS mode. The aptasensor is characterized by high reliability and specificity, among other things, to distinguish Pb2+ from other metal ions. In addition, the aptasensor can detect Pb2+ in actual water with good recovery. Compared with the single-mode aptasensor, the dual-mode aptasensor is characterized by high reliability, an extensive detection range, and high specificity.

Catalytic Assembly of DNAzyme Integrates with Primer Exchange Reaction (CDiPER) for Highly Sensitive Detection of MicroRNA

MicroRNAs (miRNAs) have significant regulatory functions in the modulation of gene expression, making them essential biomarkers for the diagnosis and prognosis of diseases. Nevertheless, the identification of miRNA poses significant difficulty in terms of its low abundance, necessitating sensitive and reliable approaches. Herein, we develop a simple approach, termed Catalytic assembly of DNAzyme integrates with Primer Exchange Reaction (CDiPER), for reliable and sensitive miRNA detection through the target recognition-triggered DNAzyme assembly and primer exchange reaction (PER) strategy. In this method, target miRNA can precisely bind with a specifically designed hairpin probe (H probe) to induce the conformation changes of the H probe, releasing DNAzyme sections to activate the PER process for signal amplification and fluorescence signal production. The established method displays a high dynamic range of over 6 orders of magnitude and a low detection limit of 312 aM. The created method has a number of unique advantages, such as (i) a better sensitivity than existing systems using PER for signal amplification as a result of its integration with the target recognition-triggered DNAzyme assembly and (ii) streamlined operating procedures. Further, the technology was used to detect the expression of miRNA in collected clinical samples from diabetes mellitus patients, revealing that miRNA was decreased in patients and demonstrating the significant clinical promise of the method.

Programmable Aptasensor for Regulating CRISPR/Cas12a Activity

CRISPR-mediated aptasensors have gained prevalence for detecting non-nucleic acid targets. However, there is an urgent need to develop an easily customizable design to improve the signal-to-noise ratio, enhance universality, and expand the detection range. In this article, we report a CRISPR-mediated programmable aptasensor (CPAS) platform. The platform includes single-stranded DNA comprising the aptamer sequence, locker DNA, and a crRNA recognition region, forming a hairpin structure through complementary hybridization. With T4 DNA polymerase, the crRNA recognition region was transformed into a complete double-stranded DNA through stem-loop extension, thereby activating the trans-cleavage activity of Cas 12a and generating fluorescence signals. The specific binding between the target molecule and aptamer disrupted the formation of the hairpin structure, altering the fluorescence signals. Notably, the CPAS platform allows for easy customization by simply changing the aptamer sequence and locker DNA, without entailing adjustments to the crRNA. The optimal number of bases in the locker DNA was determined to be seven nucleotides for the SARS-CoV-2 spike (S) protein and four nucleotides for ATP. The CPAS platform exhibited high sensitivity for S protein and ATP detection. Integration with a lateral flow assay enabled sensitive detection within 1 h, revealing its excellent potential for portable analysis.

A highly sensitive colorimetric DNA sensor for MicroRNA-155 detection: leveraging the peroxidase-like activity of copper nanoparticles in a double amplification strategy

A novel and highly sensitive colorimetric DNA sensor for determination of miRNA-155 at attomolar levelsis presented that combines the peroxidase-like activity of copper nanoparticles (CuNPs) with the hybridization chain reaction (HCR) . The utilization of CuNPs offers advantages such as strong interaction with double-stranded DNA, excellent molecular recognition, and mimic catalytic activity. Herein, a capture probe DNA (P1) was immobilized on carboxylated magnetic beads (MBs), allowing for amplified immobilization due to the 3D surface. Subsequently, the presence of the target microRNA-155 led to the formation of a sandwich structure (P2/microRNA-155/P1/MBs) when P2 was introduced to the modified P1/MBs. The HCR reaction was then triggered by adding H1 and H2 to create a super sandwich (H1/H2)n. Following this, Cu2+ ions were attracted to the negatively charged phosphate groups of the (H1/H2)n and reduced by ascorbic acid, resulting in the formation of CuNPs, which were embedded into the grooves of the (H1/H2)n. The peroxidase-like activity of CuNPs catalyzed the oxidation reaction of 3,3',5,5'-Tetramethylbenzidine (TMB), resulting in a distinct blue color measured at 630 nm. Under optimal conditions, the colorimetric biosensor exhibited a linear response to microRNA-155 concentrations ranging from 80 to 500 aM, with a detection limit of 22 aM, and discriminate against other microRNAs. It was also successfully applied to the determination of microRNA-155 levels in spiked human serum.

Smart enzyme-free amplification dual-mode self-powered platform designed on two-dimensional networked graphdiyne and DNA nanorods for ultra-sensitive detection of breast cancer biomarkers

Research has shown that microRNAs exhibit regular dysregulation in cancers, making them potential biomarkers for cancer diagnosis. However, achieving specific and sensitive detection of microRNAs has been a challenging task. To address this issue, two-dimensional networked graphdiyne is used to fabricate a self-powered biosensor and establish a new approach for ultra-responsive dual-mode detection of miRNA-141, a breast cancer biomarker. This method detects miRNA-141 using both electrochemical and colorimetric modes by measuring the output electrical signal of an enzyme-based biofuel cell and the RGB blue value of the electrolyte solution. Tetrahedral DNA and DNA nanorods also are immobilized on the electrode as a biocathode and methylene blue is used as the electron acceptor, which is fixed in the DNA phosphate backbone through electrostatic adsorption. The bioanode catalyzes the oxidation of glucose to produce electrons, which reduces methylene blue to its reduced form, resulting in a high open-circuit voltage (EOCV) and a highger RGB Blue value, enabling dual-mode detection. A reliable linear correlation is observed between EOCV values and miRNA-141 concentrations ranging from 0.0001 to 100 pM, with a detection limit of 21.9 aM (S/N = 3). Additionally, the colorimetric mode also demonstrates a reliable linear correlation with a concentration range of 0.0001-10000 pM, and this method can detect a concentration of 22.2 aM (S/N = 3). This innovative research realizes sensitive and accurate determination of miRNA-141 and provides an important new method for cancer diagnosis.

Primer Exchange Reaction Coupled with DNA-Templated Silver Nanoclusters for Label-Free and Sensitive Detection of MicroRNA

MicroRNAs (MiRNAs) play pivotal roles in regulating gene expression, and serve as crucial biomarkers for diagnosis of a variety of disease. However, label-free and sensitive miRNA detection remains a huge challenge due to the low abundance. Herein, we developed an approach through integrating primer exchange reaction (PER) with DNA-templated silver nanoclusters (AgNCs) for label-free and sensitive miRNA detection. In this method, PER was used to amplify miRNA signals and produce single-strand DNA (ssDNA) sequences. The produced ssDNA sequences mediated DNA-templated AgNCs based signal generation by unfolding the designed hairpin probe (HP). The generated AgNCs signal was correlated with the dosage of target miRNA. Eventually, the established approach exhibited a low detection of limit of 47 fM with a great dynamic range of more than five orders of magnitude. In addition, the method was also utilized to detect the miRNA-31 expression in collected clinical samples from pancreatitis patients and demonstrated that miRNA-31 was upregulated in patients, showing a great promising of the method in clinical application.

Homogeneous, Simple, and Direct Analysis of Exosomal PD-L1 via Aptamer-Bivalent-Cholesterol-Anchor Assembly of DNAzyme (ABCzyme) for Tumor Immunotherapy

Breakthroughs in immune checkpoint inhibitor (ICI) therapy have revolutionized clinical tumor therapy. Immunohistochemistry (IHC) analysis of PD-L1 in tumor tissue has been used to predict the response to tumor immunotherapy, but the results are not reproducible, and IHC is invasive and cannot be used to monitor the dynamic changes in PD-L1 expression during treatment. Monitoring the expression level of the PD-L1 protein on exosomes (exosomal PD-L1) is promising for both tumor diagnosis and tumor immunotherapy. Here, we established an aptamer-bivalent-cholesterol-anchor assembly of DNAzyme (ABCzyme) analytical strategy that can directly detect exosomal PD-L1 with a minimum lower limit of detection of 5.21 pg/mL. In this way, we found that the levels of exosomal PD-L1 are significantly elevated in the peripheral blood of patients with progressive disease. The precise analysis of exosomal PD-L1 by the proposed ABCzyme strategy provides a potentially convenient method for the dynamic monitoring of tumor progression in patients who receive immunotherapy and proves to be a potential and effective liquid biopsy method for tumor immunotherapy.

New method for microRNA detection based on multimerization

Detection of specific microRNA (miRNA) is of great demand due to their essential role in genes regulation, stress response and development of diseases. However, mature miRNAs are small molecules that make it difficult to use routine amplification-based methods. Here, we report an approach for detection of miRNA based on a new type of isothermal amplification, namely, multimerization. The proposed technique is simple and versatile, excludes a reverse transcription step, and requires two conventional primers only and no additional stem-loop or fluorogenic probes. Only mature miRNAs can initiate multimerization, thereby, pri- or pre-miRNA are excluded from analysis, ensuring high accuracy of the assay. The approach was approved on miRNA from common wheat Triticum aestivum; the increase of Tae-miRNA159 level for plants affected by Stagonospora nodorum Berk infection was demonstrated. The obtained results allow to perform quantitative analysis, providing determination of specific targets with high reliability (detection limit of about 20 pM).

A General Signal Amplifier of Self-Assembled DNA Micelles for Sensitive Quantification of Biomarkers

Owing to the excellent structural rigidity and programmable reaction sites, DNA nanostructures are more and more widely used, but they are limited by high cost, strict sequence requirements, and time-consuming preparation. Herein, a general signal amplifier based on a micelle-supported entropy-driven circuit (MEDC) was designed and prepared for sensitive quantification of biomarkers. By modifying a hydrophobic cholesterol molecule onto a hydrophilic DNA strand, the amphiphilic DNA strand was first prepared and then self-assembled into DNA micelles (DMs) driven by hydrophobic effects. The as-developed DM showed unique advantages of sequence-independence, easy preparation, and low cost. Subsequently, amplifier units DMF and DMTD were successfully fabricated by connecting fuel strands and three-strand duplexes (TDs) to DMs, respectively. Finally, the MEDC was triggered by microRNA-155 (miR-155), which herein acted as a model analyte, resulting in dynamic self-assembly of poly-DNA micelles (PDMs) and causing the recovery of cyanine 3 (Cy3) fluorescence as the DMTD dissociated. Benefiting from the "diffusion effect", the MEDC herein had a nearly 2.9-fold increase in sensitivity and a nearly 97-fold reduction in detection limit compared to conventional EDC. This amplifier exhibited excellent sensitivity of microRNAs, such as miR-155 detection in a dynamic range from 0.05 to 4 nM with a detection limit of 3.1 pM, and demonstrated outstanding selectivity with the distinguishing ability of a single-base mismatched sequence of microRNAs. Overall, the proposed strategy demonstrated that this sequence-independent DNA nanostructure improved the performance of traditional DNA probes and provided a versatile method for the development of DNA nanotechnology in biosensing.

OL-FS13 Alleviates Cerebral Ischemia-reperfusion Injury by Inhibiting miR-21-3p Expression

BACKGROUND

OL-FS13, a neuroprotective peptide derived from Odorrana livida, can alleviate cerebral ischemia-reperfusion (CI/R) injury, although the specific underlying mechanism remains to be further explored.

OBJECTIVE

The effect of miR-21-3p on the neural-protective effects of OL-FS13 was examined.

METHODS

In this study, the multiple genome sequencing analysis, double luciferase experiment, RT-qPCR, and Western blotting were used to explore the mechanism of OL-FS13.

RESULTS

Showed that over-expression of miR-21-3p against the protective effects of OL-FS13 on oxygen- glucose deprivation/re-oxygenation (OGD/R)-damaged pheochromocytoma (PC12) cells and in CI/R-injured rats. miR-21-3p was then found to target calcium/calmodulin-dependent protein kinase 2 (CAMKK2), and its overexpression inhibited the expression of CAMKK2 and phosphorylation of its downstream adenosine 5'-monophosphate (AMP)-activated protein kinase (AMPK), thereby inhibiting the therapeutic effects of OL-FS13 on OGD/R and CI/R. Inhibition of CAMKK2 also antagonized up-regulated of nuclear factor erythroid 2-related factor 2 (Nrf-2) by OL-FS13, thereby abolishing the antioxidant activity of the peptide.

CONCLUSION

Our results showed that OL-FS13 alleviated OGD/R and CI/R by inhibiting miR-21-3p to activate the CAMKK2/AMPK/Nrf-2 axis.