Ultrasensitive and multiplexed miRNA detection system with DNA-PAINT

A CRISPR/Cas13a system based on a dumbbell-shaped hairpin combined with DNA-PAINT to establish the DCP-platform for highly sensitive detection of Hantaan virus RNA

Rapid and sensitive detection of specific RNA sequences is crucial for clinical diagnosis, surveillance, and biotechnology applications. Currently, reverse transcription-quantitative polymerase chain reaction (RT-qPCR) is the gold standard for RNA detection; however, it is associated with long processing time, complex procedures, and a high false-positive rate. To address these challenges, we developed a novel sensing platform based on CRISPR/Cas13a that incorporates a dumbbell-shaped hairpin and DNA-PAINT for rapid, highly specific, and sensitive RNA analysis. By leveraging the CRISPR/Cas13a system, this platform enables the cleavage of dumbbell-shaped hairpins, which subsequently allows the cleaved primers to initiate cyclic amplification of fluorescent signals. These signals are further enhanced by the binding and dissociation phenomena inherent to DNA-PAINT technology, ultimately achieving remarkable triple signal amplification. Additionally, the system effectively discriminates Hantaan virus RNA from Seoul virus in real samples. Importantly, the platform can be easily adapted for the detection of other RNAs by simply reconfiguring the hybridization region of crRNA. In conclusion, this platform represents a "five-in-one" RNA detection approach that integrates reliability, versatility, robustness, high specificity, and superior quantitative capabilities. It provides novel insights for direct RNA detection based on CRISPR/Cas13a and demonstrates significant potential for advancement in viral diagnostics.

Dielectric Nanocavity Enhanced Fluorescence Emission for Ultrasensitive Wavelength-Multiplexed Detection

This study demonstrates a novel biosensing platform utilizing a dielectric nanocavity to enhance fluorescence emission for the ultrasensitive detection of biomolecules. By coupling a silver (Ag) nanocube with a distributed Bragg reflector (DBR) mirror, we achieved a substantial fluorescence enhancement reaching a maximum enhancement factor of up to 855-fold and having quasi-single molecule sensitivity. The platform was successfully applied for multiplexed detection of four different miRNA biomarkers, showcasing its ability to detect multiple targets simultaneously with high sensitivity. The simplicity, rapid speed, and small detection volume (down to 0.5 μL) of this system make it suitable for high-throughput and large-area nanocavity imaging. Our findings offer a promising solution for ultrasensitive, multiplexed biosensing with potential applications in disease diagnosis, personalized medicine, and digital molecular diagnostics.

Photothermal effect-assisted reduced graphene oxide biosensor for amplification-free detection of miRNA

It remains a challenge to achieve high-sensitivity detection of tumor marker miRNA using optical refractive index (RI) sensors without nucleic acid amplification. This study proposes the photothermal effect-assisted reduced graphene oxide (rGO) biosensor that combines the photothermal effect of rGO with the rGO-based RI sensor for high-sensitivity detection of tumor marker miRNA-21. The rGO was functionalized with DNA probes capable of specifically hybridizing with the target miRNA-21. Quantitative detection of miRNA-21 was achieved by monitoring the RI change caused by the competitive hybridization of single-strand DNA (ssDNA)-functionalized AuNPs and target miRNA-21 with the DNA probes on the rGO surface. The presence of AuNPs disturbed the evanescent field on the rGO surface, thus achieving signal amplification. Furthermore, the localized photothermal effect heat induced by the interaction between rGO and pump light can effectively improve the hybridization kinetics of nucleic acid chains and achieve further signal amplification. The proposed biosensor had a high sensitivity toward the target miRNA-21, achieving a low detection limit of 4.05 fM without nucleic acid amplification. Its high specificity allowed for the recognition of single-base mismatches in miRNA-21. In addition, accurate quantification of low abundance miRNA-21 spiked into human urine samples was also successfully achieved. The photothermal effect-assisted rGO biosensor offers a promising approach for high-sensitivity detection of tumor marker miRNA without need for nucleic acid amplification.

Robust nCuO modulated by defect engineering enhanced photoelectrochemical biosensor for the detection of miRNA-21

Traditional p-type CuO (pCuO), valued for its tunable band gap and p-type conductivity, has been widely used in photoelectrochemical biosensors. However, its weak conductivity leads to unsatisfied photoelectrochemical signals and limits its use in in situ vulcanization reactions. We synthesized n-type CuO (nCuO) with abundant oxygen vacancies through a simple chemical reduction for the first time, which was applied as efficient photoactive material. The resulting nCuO exhibits superior photoelectrochemical performance than pCuO, thanks to enhanced carrier separation facilitated by the oxygen vacancies. Upon miRNA-21 introduction, H₂S was generated, which can react with Cu(II) to form nCuO-pCuS heterojunction on the electrode. Inspiringly, the current increase of nCuO is 2.3 times higher than the pCuO after vulcanization reaction due to the built-in electric field of the nCuO-pCuS heterojunction can promote efficient carrier separation. Under optimal conditions, the biosensor offers excellent analytical performance, with a wide linear range (0.004-400 pM) and a detection limit of 1.8 fM. The integration of oxygen defect engineering and target-triggered vulcanization presents a new strategy for designing high-performance photoelectrochemical biosensors.

Exonuclease-III Assisted Signal Cycle Integrating with Self-Priming Mediated Chain Extension for Sensitive and Reliable MicroRNA Detection

MicroRNA (miRNA) is pivotal in regulating pathological progression and may serve as a significant biomarker for early diagnosis, treatment, and management strategies for atherosclerosis. This study produced a self-priming amplification-accelerated CRISPR/Cas system-based method for the sensitive and selective detection of miRNA by merging Exo-III-assisted target recycling, self-priming-mediated chain extension, and the CRISPR/Cas12a system. The sensor comprises three stages: (i) the creation of a substrate template via Exo-III mediated target recycling and DNA ligase assisted ligation; (ii) the exponential isothermal reaction facilitated by DNA polymerase for signal amplification; (iii) the trans-cleavage activity of CRISPR/Cas12a after recognizing the amplification product generates signals. We employed miRNA-21 as a target. The strategy enables sensitive detection of miRNA-21 without the use of primers, and the unique design of the CRISPR/sgRNA complex efficiently mitigates background signal interference. The sensor can recognize single-base mutant homologous sequences and demonstrate a steady performance in complicated biological matrices. This sensor has been effectively employed to precisely assess miRNA-21 in engineered clinical samples, showcasing its significant potential in clinical diagnostics and of atherosclerosis.

Label-free (fluorescence-free) sensing of a single DNA molecule on DNA origami using a plasmon-enhanced WGM sensor

The integration of DNA origami structures with opto-plasmonic whispering gallery mode (WGM) sensors offers a significant advancement in label-free biosensing, overcoming the limitations of traditional fluorescence-based techniques, and providing enhanced sensitivity and specificity for detecting DNA hybridization events. In this study, DNA origami acts as a scaffold for the precise assembly of plasmonic dimers, composed of gold nanorods (AuNRs), which amplify detection sensitivity by generating strong near-field enhancements in the nanogap between the nanorods. By leveraging the strong electromagnetic fields generated within the nanogap of the plasmonic dimer, this platform enables the detection of transient hybridization events between DNA docking strands and freely diffusing complementary sequences. Our findings demonstrate that the salt concentration critically influences DNA hybridization kinetics. Higher ionic strengths reduce electrostatic repulsion between negatively charged DNA strands, thereby stabilizing duplex formation and prolonging interaction times. These effects are most pronounced at salt concentrations around 300-500 mM, where optimal conditions for duplex stability and reduced dissociation rates are achieved. By thoroughly investigating the hybridization kinetics under varying environmental conditions, this study contributes to a deeper understanding of DNA interactions and offers a robust tool for single-molecule detection with real-time capabilities.

LRET-Based Simultaneous Detection of Dual miRNAs via Multitrap Optical Tweezers Assisted Suspension Array Tagged by Two Different Luminescent Quenchable UCNPs Combining CRISPR/Cas12a Amplification

Nowadays, optical tweezers play a vital role not only in optical manipulation but also in bioassay. As principal optical trapping objects, microbeads can combine optical tweezers with suspension array technology, with amply focused laser beams and adequately concentrated tags contributing to highly sensitive detection. In view of the inefficiency of conventional single-trap optical tweezers, multitrap systems are developed. Here, green- and blue-emitting core-shell-shell upconversion nanoparticles (UCNPs) are adopted to encode microbeads and determine dual miRNAs, with the internal shells leading the luminescence process to facilitate quenching through luminescence resonance energy transfer (LRET). Utilizing the trans cleavage of CRISPR/Cas12a, quenched luminescence signals are recovered and amplified, causing further enhanced detection sensitivity. Ultimately, limits of detection (LOD) of 17 and 22 aM are obtained with excellent specificities verified. Furthermore, dual miRNAs from MCF-7, A549, and MCF-10A cells are extracted and detected, with results consistent with those obtained by PCR. Notably, miR-155 in MCF-7 and A549 cells is detectable at the single-cell level. Thus, the differences in the measured miRNA levels between MCF-7 and MCF-10A cells imply the potential of this method to discriminate breast cancer cells from epithelial cells despite the difficulty in distinguishing different cancer cells due to similar miRNA levels.

Ultrasensitive detection of cancer-associated nucleic acids and mutations by primer exchange reaction-based signal amplification and flow cytometry

The detection of cancer-associated nucleic acids and mutations through liquid biopsy has emerged as a highly promising non-invasive approach for early cancer detection and monitoring. In this study, we report the development of primer exchange reaction (PER) based signal amplification strategy that enables the rapid, sensitive and specific detection of nucleic acids bearing cancer specific single nucleotide mutations using flow cytometry. Using micrometer size beads as support for immobilizing oligonucleotides and programmable PER assembly for target oligonucleotide recognition and fluorescence signal amplification, we demonstrated the versatile detection of target nucleic acids including KRAS oligonucleotide, fragmented mRNAs, and miR-21. Moreover, our detection system can discriminate single base mutations frequently occurred in cancer-associated genes including KRAS, PIK3CA and P53 from cell extracts and circulating tumor DNAs (ctDNAs). The detection is highly sensitive, with a limit of detection down to 27 fM without pre-amplification. In view of a clinical application, we demonstrate the detection of single mutations after extraction and pre-amplification of ctDNAs from the plasma of breast cancer patients. Importantly, our detection strategy enabled the detection of single KRAS mutation even in the presence of 1000-fold excess of wild type (WT) DNA using multi-color flow cytometry detection approach. Overall, our strategy holds immense potential for clinical applications, offering significant improvements for early cancer detection and monitoring.

MiRS-HF: A Novel Deep Learning Predictor for Cancer Classification and miRNA Expression Patterns

Cancer classification and biomarker identification are crucial for guiding personalized treatment. To make effective use of miRNA associations and expression data, we have developed a deep learning model for cancer classification and biomarker identification. We propose an approach for cancer classification called MiRNA Selection and Hybrid Fusion (MiRS-HF), which consists of early fusion and intermediate fusion. The early fusion involves applying a Layer Attention Graph Convolutional Network (LAGCN) to a miRNA-disease heterogeneous network, resulting in a miRNA-disease association degree score matrix. The intermediate fusion employs a Graph Convolutional Network (GCN) in the classification tasks, weighting the expression data based on the miRNA-disease association degree score. Furthermore, MiRS-HF can identify the important miRNA biomarkers and their expression patterns. The proposed method demonstrates superior performance in the classification tasks of six cancers compared to other methods. Simultaneously, we incorporated the feature weighting strategy into the comparison algorithm, leading to a significant improvement in the algorithm's results, highlighting the extreme importance of this strategy.

A Graphene Oxide-based Assay for Sensitive Osteonecrosis of the Femoral Head (ONFH) related microRNA Detection via Exonuclease-III Assisted Dual Signal Cycle

Accurate detection of circulating microRNAs (miRNAs) plays a vital role in the diagnosis of various diseases. The current miRNA detection methods, however, are widely criticized for their low sensitivity and excessive background signal. Herein, we propose a graphene oxide (GO) based fluorescent biosensor for sensitive and reliable miRNA analysis with a low background signal by utilizing exonuclease III (Exo III)-assisted target recycling and hybridization chain reaction (HCR). To initiate Exo-III-assisted dual signal cycles, a hairpin DNA probe (H probe) was developed for selective miRNA binding. Dye quenching occurred when carboxyfluorescein (FAM)-labeled hairpins (HP1 and HP1) were unable to bind to their intended target and instead adsorb onto the surface of GO via p-stacking interactions. Exo III sequentially cleaved the 3'-strand of the H probe and the S probe upon attachment of the target miRNA, resulting in the release of the miRNA and the autonomous production of a "g" sequence. The released target miRNA then hybridized with a second H probe and progressed to the subsequent reaction phase. With the help of the HP1 and HP2 probes, a lengthy dsDNA product was produced when the "g" sequence triggered HCR. The dsDNA product was not absorbed by GO, and the material instead fluoresced brightly. As a result, the amount of miRNA of interest was measured. With a LOD of only 5.6 fM, this bioassay demonstrated excellent selectivity and great sensitivity.

A DNA walker based on hairpin-shaped DNA aligner and fueled by nicking endonuclease for sensitive and rapid miRNA analysis

BACKGROUND

DNA walker-based strategies have gained significant attention in nucleic acid analysis. However, they face challenges related to balancing design complexity, sequence dependence, and amplification efficiency. Furthermore, most existing DNA walkers rely on walking and lock probes, requiring optimization of various parameters like DNA probe sequence, walking-to-lock probe ratio, lock probe length, etc. to achieve optimal performance. This optimization process is time-consuming and adds complexity to experiments. To enhance the performance and reliability of DNA walker nanomachines, there is a need for a simpler, highly sensitive, and selective alternative strategy.

RESULTS

A sensitive and rapid miRNA analysis strategy named hairpin-shaped DNA aligner and nicking endonuclease-fueled DNA walker (HDA-NE DNA walker) was developed. The HDA-NE DNA walker was constructed by modifying hairpin-shaped DNA aligner (HDA) probe and substrate report (SR) probe on the surface of AuNPs. Under normal conditions, HDA and SR remained stable. However, in the presence of miR-373, HDA underwent a conformational transition to an activated structure to continuously cleave the SR probe on the AuNPs with the assistance of Nt.AlwI nicking endonuclease, resulting in sensitive miRNA detection with a detection limit as low as 0.23 pM. Additionally, the proposed HDA-NE DNA walker exhibited high selectivity in distinguishing miRNAs with single base differences and can effectively analyze miR-373 levels in both normal and breast cancer patient serums.

SIGNIFICANCE

The proposed HDA-NE DNA walker system was activated by a conformational change of HDA probe only in the presence of the target miRNA, eliminating the need for a lock probe and without sequence dependence for SR probe. This strategy demonstrated a rapid reaction rate of only 30 min, minimal background noise, and a high signal-to-noise ratio (S/B) compared to capture/lock-based DNA walker. The method is expected to become a powerful tool and play an important role in disease diagnosis and precision therapy.

Functionalized DNA Origami-Enabled Detection of Biomarkers

Biomarkers are crucial physiological and pathological indicators in the host. Over the years, numerous detection methods have been developed for biomarkers, given their significant potential in various biological and biomedical applications. Among these, the detection system based on functionalized DNA origami has emerged as a promising approach due to its precise control over sensing modules, enabling sensitive, specific, and programmable biomarker detection. We summarize the advancements in biomarker detection using functionalized DNA origami, focusing on strategies for DNA origami functionalization, mechanisms of biomarker recognition, and applications in disease diagnosis and monitoring. These applications are organized into sections based on the type of biomarkers - nucleic acids, proteins, small molecules, and ions - and concludes with a discussion on the advantages and challenges associated with using functionalized DNA origami systems for biomarker detection.

Electrochemical detection of miRNA using commercial and hand-made screen-printed electrodes: liquid biopsy for cancer management as case of study

The growth of liquid biopsy, i. e., the possibility of obtaining health information by analysing circulating species (nucleic acids, cells, proteins, and vesicles) in peripheric biofluids, is pushing the field of sensors and biosensors beyond the limit to provide decentralised solutions for nonspecialists. In particular, among all the circulating species that can be adopted in managing cancer evolution, both for diagnostic and prognostic applications, microRNAs have been highly studied and detected. The development of electrochemical devices is particularly relevant for liquid biopsy purposes, and the screen-printed electrodes (SPEs) represent one of the building blocks for producing novel portable devices. In this work, we have taken miR-2115-3p as model target (it is related to lung cancer), and we have developed a biosensor by exploiting the use of a complementary DNA probe modified with methylene blue as redox mediator. In particular, the chosen sensing architecture was applied to serum measurements of the selected miRNA, obtaining a detection limit within the low nanomolar range; in addition, various platforms were interrogated, namely commercial and hand-made SPEs, with the aim of providing the reader with some insights about the optimal platform to be used by considering both the cost and the analytical performance.

Sample-to-answer salivary miRNA testing: New frontiers in point-of-care diagnostic technologies

MicroRNA (miRNA), crucial non-coding RNAs, have emerged as key biomarkers in molecular diagnostics, prognosis, and personalized medicine due to their significant role in gene expression regulation. Salivary miRNA, in particular, stands out for its non-invasive collection method and ease of accessibility, offering promising avenues for the development of point-of-care diagnostics for a spectrum of diseases, including cancer, neurodegenerative disorders, and infectious diseases. Such development promises rapid and precise diagnosis, enabling timely treatment. Despite significant advancements in salivary miRNA-based testing, challenges persist in the quantification, multiplexing, sensitivity, and specificity, particularly for miRNA at low concentrations in complex biological mixtures. This work delves into these challenges, focusing on the development and application of salivary miRNA tests for point-of-care use. We explore the biogenesis of salivary miRNA and analyze their quantitative expression and their disease relevance in cancer, infection, and neurodegenerative disorders. We also examined recent progress in miRNA extraction, amplification, and multiplexed detection methods. This study offers a comprehensive view of the development of salivary miRNA-based point-of-care testing (POCT). Its successful advancement could revolutionize the early detection, monitoring, and management of various conditions, enhancing healthcare outcomes. This article is categorized under: Diagnostic Tools > Biosensing Diagnostic Tools > Diagnostic Nanodevices.

An ultrasensitive and multiplexed miRNA one-step real time RT-qPCR detection system and its application in esophageal cancer serum

MicroRNAs (miRNAs) are increasingly recognized as promising biomarkers for early disease diagnosis and prognosis. Therefore, the need for rapid, robust methods for multiplex miRNA detection in biological research and clinical diagnosis is crucial. This study introduces a novel multiplex miRNA detection method, SMOS-qPCR (Sensitive and Multiplexed One-Step RT-qPCR). The method integrates multiplexed reverse transcription and TaqMan-based qPCR into a single tube, employing a one-step operation on a real-time PCR system. We investigated the effect of 3' end phosphorylation of the Linker, Linker concentration and probe concentration on the SMOS-qPCR, resulted in a wide linear range from 1 fM to 0.1 zM (R2 ≥ 0.99 for each miRNA), surpassing the capabilities of stem-loop RT-qPCR and SYBR Green One-step RT-qPCR. The method showed excellent performance in distinguishing mature miRNA from miRNA precursor, and successfully detected four miRNAs in a single tube without cross-interference. Its high specificity enables precise differentiation of less than 1% nonspecific signal. Finally, we demonstrated the effectiveness of the SMOS-qPCR system in detecting circulating miRNAs in serum samples, distinguishing between esophageal cancers and health individuals with high AUC values (>0.940). In conclusion, the proposed SMOS-qPCR system offers a straightforward and promising approach for miRNA profiling in future clinical applications.

Continuous Monitoring Biosensing Mediated by Single-Molecule Plasmon-Enhanced Fluorescence in Complex Matrices

Continuous detection of critical markers directly at the point of interest and in undiluted biological fluids represents the next fundamental step in biosensing. The goal of realizing such a platform is utterly challenging because it requires a reversible biosensor that enables the tracking of pico- to nanomolar molecular concentrations over long time spans in a compact device. Here we describe a sensing method based on plasmon-enhanced fluorescence capable of single-molecule detection of unlabeled analyte by employing biofunctionalized gold nanoparticles. The very strong plasmon-enhanced fluorescence signals allow for single-molecule sensing in unaltered biological media, while the use of low-affinity interactions ensures the continuous tracking of increasing and decreasing analyte concentrations with picomolar sensitivity. We demonstrate the use of a sandwich assay for a DNA cancer marker with a limit of detection of picomolar and a time response of 10 min. The enhanced single-molecule signals will allow for miniaturization into a small and cheap platform with multiplexing capability for application in point-of-care diagnostics, monitoring of industrial processes, and safe keeping of the environment.

DNA-based molecular recognition system for lactoferrin biosensing

The paper describes the development of a novel DNA oligonucleotide-based affinity bioreceptor that binds to lactoferrin, a glycoprotein-type immunomodulator. The research was performed using surface plasmon resonance method to investigate affinity of various types of oligonucleotides to the target protein. The 72 base pair-long 5'[(TAGAGGATCAAA)AAA]4TAGAGGATCAAA3' sequence with the highest affinity to lactoferrin was selected for further investigations. Kinetic analysis of the interaction between selected DNA and lactoferrin provided rate and equilibrium constants: ka = (2.49 ± 0.03)∙104 M-1∙s-1, kd = (1.89 ± 0.02)∙10-3 s-1, KA = (0.13 ± 0.05)∙108 M-1, and KD = (7.61 ± 0.18)∙10-8 M. Thermodynamic study conducted to determine the ΔH0, ΔS0, and ΔG0 for van't Hoff characteristic in the temperature range of 291.15-305.15 K, revealed the complex formation as endothermic and entropically driven. The chosen DNA sequence's selectivity towards lactoferrin was confirmed with interferents' response constituting <3 % of the response to lactoferrin. SPR analysis justified utility of the designed DNA oligonucleotide for Lf determination, with LOD of 4.42∙10-9 M. Finally, the interaction between lactoferrin and DNA was confirmed by electrochemical impedance spectroscopy, providing the basis for further quantitative assay of lactoferrin using the developed DNA-based bioreceptor. The interactions were performed under immobilized DNA ligand conditions, thus reflecting the sensor's surface, which facilitates their transfer to other label-free biosensor technologies.

Practical magnetic bead-based capillary electrophoresis with laser-induced fluorescence for detecting endogenous miRNA in plasma

MicroRNAs (miRNAs) are small, non-coding RNAs crucial for gene regulation and implicated in various human diseases. Their potential as clinical prognostic and diagnostic biomarkers in biological fluids necessitates reliable detection methods. In this study, a combination of streptavidin-coupled magnetic beads and capillary electrophoresis with laser-induced fluorescence (CE-LIF) was used to extract and analyze plasma miRNAs. Specifically, miRNAs hybridized with a biotinylated fluorescent DNA probe were isolated from plasma using magnetic beads. These hybridized miRNAs were then directly injected into the CE-LIF system for analysis, eliminating the need for additional processing steps. Both the hybridization and bead-to-probe binding were executed concurrently, regulated by temperature and time. Through the optimization of magnetic bead extraction and CE-LIF conditions, we developed a highly sensitive assay for miR-21 quantification in plasma. The assay displayed remarkable linearity (R2 = 0.9975) within a 0.1-5 pM range and exhibited favorable precision (0.22-1.26 %) and accuracy (98.31-111.19 %). Importantly, we successfully detected endogenous miR-21 in plasma samples from both a lung cancer patient and healthy adults, revealing a 1.7-fold overexpression of miR-21 in lung cancer plasma relative to normal samples. Our findings suggest that this developed system offers a simple and sensitive approach for detecting endogenous miRNAs in plasma, showing its potential utility in disease diagnostics. To our knowledge, this is the first study to utilize CE-LIF for plasma miRNA detection.

Amplification-free microRNA profiling with femtomolar sensitivity on a plasmonic enhanced fluorescence nano-chip

MicroRNAs (miRNAs) are a class of small, non-coding RNA molecules involved in the regulation of gene expression, thus considered as promising biomarkers for cancer, cardiovascular diseases, neurodegenerative diseases, etc. However, quantitative analysis of miRNAs faces challenges owing to their high homology, small size & ultra-low abundance, and disease occurrence is often related to abnormal expression of multiple miRNAs where method for parallel miRNAs analysis is required. In this work, multiplexed analysis of miRNAs was established on a plasmonic nano-chip capable of fluorescence enhancement in the near-infrared region. Combined with polyadenylation at the hydroxyl terminate of target miRNA to afford abundant sites for fluorophore labeling, our assay achieved amplification-free detection of miRNAs from nM to fM with the limit of detection down to ca. 5 fM. A miRNA panel was constructed to detect 10 miRNAs differentially expressed in MCF-7 and A549 cell lines and validated with qRT-PCR, demonstrating the practical application of this method. This scalable platform can be customized for different miRNA panels, facilitating multiple miRNA profiling for various diseases.

Triple ligation-based formation of a G-quadruplex for simultaneous detection of multiple miRNAs

The simultaneous detection of multiple microRNAs (miRNA) is of great necessity but has not been extensively studied. This prompted our study, which involved the development of a triple ligation-based system for detecting three miRNAs at the same time. We designed a multi-ligation-padlock (MLP) probe that consists of three parts, each of which is complementary to two different miRNAs at the same time. In the presence of all three miRNAs, the probe becomes circularized, but in the absence of even one target, the probe remains linear. The first part of the MLP probe (MLP1) contains a T7 promoter part that can initiate RNA synthesis for any given target condition. However, it also includes a G-quadruplex complementary segment, which can only form a parallel RNA G-quadruplex through rolling circle transcription by the circularized template in the presence of all three targets. In this case, the application of our parallel G-quadruplex sensing fluorescent probe lutidine DESA (LutD) produces a strong signal. However, in the absence of any one of the targets, the RNA G-quadruplex cannot be formed and ultimately the LutD probe does not generate any signal. This difference in the signal intensity represents the presence or absence of all the target miRNAs. With our system, we were able to detect miRNA 21 at levels as low as 1.13 fM, miRNA 146a as low as 1.37 fM, and miRNA 25b as low as 1.51 fM within 45 minutes, confirming that our novel system can selectively and sensitively diagnose triple miRNAs.

Light-Up Split Broccoli Aptamer as a Versatile Tool for RNA Assembly Monitoring in Cell-Free TX-TL Systems, Hybrid RNA/DNA Origami Tagging and DNA Biosensing

Binary light-up aptamers are intriguing and emerging tools with potential in different fields. Herein, we demonstrate the versatility of a split Broccoli aptamer system able to turn on the fluorescence signal only in the presence of a complementary sequence. First, an RNA three-way junction harbouring the split system is assembled in an E. coli-based cell-free TX-TL system where the folding of the functional aptamer is demonstrated. Then, the same strategy is introduced into a 'bio-orthogonal' hybrid RNA/DNA rectangle origami characterized by atomic force microscopy: the activation of the split system through the origami self-assembly is demonstrated. Finally, our system is successfully used to detect the femtomoles of a Campylobacter spp. DNA target sequence. Potential applications of our system include the real-time monitoring of the self-assembly of nucleic-acid-based devices in vivo and of the intracellular delivery of therapeutic nanostructures, as well as the in vitro and in vivo detection of different DNA/RNA targets.