Two-Temperature Hybridization for Microarray Detection of Label-Free MicroRNAs with Attomole Detection and Superior Specificity

Sensitive fluorescence detection of miRNA-124 in cardiomyocytes under oxidative stress using a nucleic acid probe

MicroRNAs (miRNAs) are small noncoding RNAs of 18-25 bases. miRNAs are also important new biomarkers that can be used for disease diagnosis in the future. Studies have shown that miR-124 levels are significantly elevated during acute myocardial infarction (AMI) and play a key role in the cardiovascular system. A variety of methods have been established to detect myocardial infarction-related miRNAs. However, most require complex miRNA extraction and isolation, and these methods are virtually undetectable when RNA levels are low in the sample. It may lead to biased results. Thus, it is necessary to develop a technique that can detect miRNA without extracting it, which means that intracellular detection is of great significance. Here, we improved the traditional silicon spheres and obtained a biosensor that could effectively capture and detect specific noncoding nucleic acids through the layer-by-layer assembly method. The sensor is protected by hyaluronic acid so it can successfully escape the lysosome into the cell and achieve detection. With the help of a full-featured microplate reader, we determined that the detection limit of the biosensor could reach 1 fM, meeting the needs of intracellular detection. At the same time, we prepared an oxidative stress cardiomyocyte infarction model and successfully captured the overexpressed miR-124 in the infarcted cells to achieve in situ detection. This study could provide a new potential tool to develop miRNAs for sensitive diagnosis in AMI, and the proposed strategy implies its potential for biomedical research.

Recent progress in Surface-Enhanced Raman Spectroscopy detection of biomarkers in liquid biopsy for breast cancer

Breast cancer is the most commonly diagnosed cancer in women globally and a leading cause of cancer-related mortality. However, current detection methods, such as X-rays, ultrasound, CT scans, MRI, and mammography, have their limitations. Recently, with the advancements in precision medicine and technologies like artificial intelligence, liquid biopsy, specifically utilizing Surface-Enhanced Raman Spectroscopy (SERS), has emerged as a promising approach to detect breast cancer. Liquid biopsy, as a minimally invasive technique, can provide a temporal reflection of breast cancer occurrence and progression, along with a spatial representation of overall tumor information. SERS has been extensively employed for biomarker detection, owing to its numerous advantages such as high sensitivity, minimal sample requirements, strong multi-detection ability, and controllable background interference. This paper presents a comprehensive review of the latest research on the application of SERS in the detection of breast cancer biomarkers, including exosomes, circulating tumor cells (CTCs), miRNA, proteins and others. The aim of this review is to provide valuable insights into the potential of SERS technology for early breast cancer diagnosis.

Recent Advances in Electrochemiluminescence Biosensors for MicroRNA Detection

Electrochemiluminescence (ECL) as an analytical technology with a perfect combination of electrochemistry and spectroscopy has received considerable attention in bioanalysis due to its high sensitivity and broad dynamic range. Given the selectivity of bio-recognition elements and the high sensitivity of the ECL analysis technique, ECL biosensors are powerful platforms for the sensitive detection of biomarkers, achieving the accurate prognosis and diagnosis of diseases. MicroRNAs (miRNAs) are crucial biomarkers involved in a variety of physiological and pathological processes, whose aberrant expression is often related to serious diseases, especially cancers. ECL biosensors can fulfill the highly sensitive and selective requirements for accurate miRNA detection, prompting this review. The ECL mechanisms are initially introduced and subsequently categorize the ECL biosensors for miRNA detection in terms of the quenching agents. Furthermore, the work highlights the signal amplification strategies for enhancing ECL signal to improve the sensitivity of miRNA detection and finally concludes by looking at the challenges and opportunities in ECL biosensors for miRNA detection.

All-in-one nanoflare biosensor combined with catalyzed hairpin assembly amplification for in situ and sensitive exosomal miRNA detection and cancer classification

Exosomal miRNAs can reflect tumor progression and metastasis, and are effective biomarkers for cancer diagnosis. However, the accuracy of exosomal miRNA-based cancer diagnosis is limited by the low sensitivity and complicated RNA extraction of traditional approaches. Herein, a novel biosensor is developed for in situ, extraction-free, and highly sensitive analysis of exosomal miRNAs via nanoflare combined with catalyzed hairpin assembly (CHA) amplification. Without cumbersome and costly miRNA extraction or transfection agents, nanoflare can directly enter the exosomes to bind target miRNAs and generate a fluorescence signal that can be amplified by the CHA reaction to achieve the in situ and highly sensitive detection of exosomal miRNAs. Under the optimal conditions, the detection limit of 5 aM is obtained for three exosomal miRNAs, which is an order of magnitude lower than quantitative real time polymerase chain reaction (qRT-PCR). In combination with the linear discriminant analysis algorithm, five exosomes are distinguished with 100% accuracy. Importantly, five cancers including breast, lung, liver, cervical, and colon cancer from 64 patients are distinguished with 99% accuracy by testing exosomal miRNAs in clinical plasma. This simple, accurate, and sensitive biosensor holds the potential to be expanded into clinical non-invasive cancer diagnostic tests.

Progress in quantum dot-based biosensors for microRNA assay: A review

MicroRNAs (miRNAs) are responsible for post-transcriptional gene regulation, and may function as valuable biomarkers for diseases diagnosis. Accurate and sensitive analysis of miRNAs is in great demand. Quantum dots (QDs) are semiconductor nanomaterials with superior optoelectronic features, such as high quantum yield and brightness, broad absorption and narrow emission, long fluorescence lifetime, and good photostability. Herein, we give a comprehensive review about QD-based biosensors for miRNA assay. Different QD-based biosensors for miRNA assay are classified by the signal types including fluorescent, electrochemical, electrochemiluminescent, and photoelectrochemical outputs. We highlight the features, principles, and performances of the emerging miRNA biosensors, and emphasize the challenges and perspectives in this field.

Diagnosis Biomarkers of Cholangiocarcinoma in Human Bile: An Evidence-Based Study

Simple Summary

A liquid biopsy has the characteristics of low trauma and easy acquisition in the diagnosis of cholangiocarcinoma. Many researchers try to find diagnostic or prognostic biomarkers of CCA through blood, urine, bile and other body fluids. Due to the close proximity of bile to the lesion and the stable nature, bile gradually comes into people’s view. The evaluation of human bile diagnostic biomarkers is not only to the benefit of screening more suitable clinical markers but also of exploring the pathological changes of the disease.

Abstract

Cholangiocarcinoma (CCA) is a multifactorial malignant tumor of the biliary tract, and the incidence of CCA is increasing in recent years. At present, the diagnosis of CCA mainly depends on imaging and invasive examination, with limited specificity and sensitivity and late detection. The early diagnosis of CCA always faces the dilemma of lacking specific diagnostic biomarkers. Non-invasive methods to assess the degree of CAA have been developed throughout the last decades. Among the many specimens looking for CCA biomarkers, bile has gotten a lot of attention lately. This paper mainly summarizes the recent developments in the current research on the diagnostic biomarkers for CCA in human bile at the levels of the gene, protein, metabolite, extracellular vesicles and volatile organic compounds.

Self-Propelled Janus Mesoporous Micromotor for Enhanced MicroRNA Capture and Amplified Detection in Complex Biological Samples

The slow mass transport of the target molecule essentially limits the biosensing performance. Here, we report a Janus mesoporous microsphere/Pt-based (meso-MS/Pt) nanostructure with greatly enhanced target transport and accelerated recognition process for microRNA (miRNA) amplified detection in complex biological samples. The mesoporous MS was synthesized via double emulsion interfacial polymerization, and Pt nanoparticles (PtNPs) were deposited on the half-MS surface to construct Janus meso-MS/Pt micromotor. The heterogeneous meso-MS/Pt with a large surface available was attached to an entropy-driven DNA recognition system, termed meso-MS/Pt/DNA, and the tremendous pores network was beneficial to enhanced receptor-target interaction. It enabled moving around complex biological samples to greatly enhance target miRNA mass transport and accelerate recognition procedure due to the self-diffusiophoretic propulsion. Coupling with the entropy-driven signal amplification, extremely sensitive miRNA detection in Dulbecco's modified Eagle medium (DMEM), and cell lysate without preparatory and washing steps was realized. Given the free preparatory and washing steps, fast mass transport, and amplified capability, the meso-MS/Pt/DNA micromotor provides a promising method for miRNAs analysis in real biological samples.

Catalytic Hairpin Assembly-Driven Ratiometric Dual-Signal Electrochemical Biosensor for Ultrasensitive Detection of MicroRNA Based on the Ratios of Fe-MOFs and MB-GA-UiO-66-NH2

In this work, a novel ratio electrochemical biosensing platform based on catalytic hairpin assembly target recovery to trigger dual-signal output was developed for ultrasensitive detection of microRNA (miRNA). To achieve the ratiometric dual-signal strategy, methylene blue (MB), an electrochemical indicator, was ingeniously loaded into the pores of graphene aerogel (GA) and metal-organic framework (MOF) composites with high porosity and large specific surface area, and another electrochemical indicator Fe-MOFs with distinct separation of redox potential was selected as a signal probe. Concretely, with the presence of the target miRNA, the CHA process was initiated and the signal probe was introduced to the electrode surface, producing abundant double-stranded H1-H2@Fe-MOFs-NH₂. Then, the measurement and analysis of the prepared ratiometric electrochemical biosensor by differential pulse voltammetry (DPV) showed that the introduction of the target miRNA led to an increase in the oxidation peak signal of Fe-MOFs (+0.8 V) and a decrease in the oxidation peak signal of MB (-0.23 V). Therefore, the peak current ratio of I_Fe-MOFs/I_MB could be employed to accurately reflect the actual concentration of miRNA. Under optimal conditions, the detection limit of the proposed biosensor was down to 50 aM. It was worth noting that the proposed biosensor exhibited excellent detection performance in a complex serum environment and tumor cell lysates, showing great potential in biosensing and clinical diagnosis.

Monitoring Clinical-Pathological Grading of Hepatocellular Carcinoma Using MicroRNA-Guided Semiconducting Polymer Dots

MicroRNAs (miRNAs) are a class of small, noncoding RNAs involved in nearly all genetic central dogma processes and human biological behavior, which also play a significant role in the pathological activity of tumors, such as gene transcription, protein translation, and exosome secretion. Therefore, through the navigation of certain specific miRNAs, we can trace the specific physiological processes or image some specific tissues. Designing and accurately positioning microRNA (miRNA)-sensitive fluorescent nanoprobes with benign specificity and recognition in cells or tissues are a challenging research field. To solve the difficulties, we introduce four semiconducting polymer dots (Pdots) as nanoprobes linked by specific miRNA antisense sequences for monitoring the pathological grading by the variation in miRNA expression. Based on the base pairing principle, these miRNA-sensitive Pdots could bind to specific miRNAs within the cancerous cells. As impacted by the background of different pathology gradings, the proportions of the four hepatocellular carcinoma (HCC)-specific miRNAs within the cancerous cell are different, and the pathological grading of the patient tissues can be determined by comparing the palette combinations. The short single-stranded RNA-functionalized Pdots, which have excellent microRNA sensitivity, are observed in an experimental cell model and a series of tissue specimens from HCC patients for the first time. Using the Förster (or fluorescence) resonance energy transfer (FRET) model of Pdots and Cy3dt tag to simulate in vivo miRNA detection, the superior sensitivity and specificity of these nanoprobes are verified. The interference of subjective factors in traditional single/bis-dye emission intensity detection is abandoned, and multiple label staining is used to enhance sensitivity further and reduce the false-positive rate. The feasibility exhibited by this novel staining method is verified in normal hepatocellular HCC cell lines and 16 frozen ultrathin tissue sections, which are employed to quantify pathological grading-related color presentation systems for clinical doctors and pathologists' use. The intelligently designed miRNA-guided Pdots will emerge as an ideal platform with promising biological imaging.

Rapid and ultrasensitive detection of DNA and microRNA-21 using a zirconium porphyrin metal-organic framework-based switch fluorescence biosensor

Sensitive and accurate detection of nucleic acid biomarkers is critical for early cancer diagnosis, disease monitoring, and clinical treatment. In this study, we developed a switch fluorescence biosensor for simple and high-efficient detection of nucleic acid biomarkers using 6-carboxyfluorescein (FAM)-modified single-stranded DNA (ssDNA) probes (FAM-P1/P2), and zirconium porphyrin metal-organic framework nanoparticles (ZrMOF) acted as fluorescence quencher. FAM-P1/P2 probes were adsorbed on ZrMOF surface because of π-π stacking, hydrogen bonding, and electrostatic interactions. Fluorescence quenching event occurred by fluorescence resonance energy transfer (FRET) and photo-induced electron transfer (PET) processes, thereby achieving the "off" fluorescence status. Once the specific binding was formed between the fluorescence probes and the targets, the rigid double-stranded DNA (dsDNA) structures were released from ZrMOF surface, resulting in the recovery of fluorescence and the "on" status. Because of the superior adsorption ability of ZrMOF toward ssDNA than dsDNA, the switch of fluorescence signals from "off" to "on" allowed rapid and ultrasensitive detection of ssDNA (T1) and microRNA-21 (miR-21) within 30 min. The limit of detection (signal-to-noise ratio = 3) for T1 and miR-21 were 2 fM and 11 aM, respectively. Moreover, the proposed strategy was very simple as it worked by the facile adsorption-quenching-recovery mechanism without difficult and complicated immobilization processes. Also, this biosensor showed an excellent analytical performance in the detection of miR-21 in human serum samples. Therefore, this biosensor might be considered a potential tool for the detection of DNA and miRNA biomarkers in clinical samples.

A fluorescence strategy for circRNA quantification in tumor cells based on T7 nuclease-assisted cycling enzymatic amplification

Circular Ribonucleic Acid (CircRNA) plays regulatory roles in many biological processes, such as tumors and metabolic diseases. Due to the fact that circRNA is more stable and conservative than linear RNA, circRNA has become a potential biomarker in early clinical diagnosis and biomedical research. Therefore, the quantification of circRNA expression level is of importance for understanding their functions and their applications for disease diagnosis and treatment. Nevertheless, due to the low abundance of circRNA, it is still a challenge for the analysis of circRNA in cells. Herein, we proposed a sensitive detection method for circRNA based on the T7 exonuclease-assisted cycling enzymatic amplification. The fluorescent sensor was constructed by a hairpin molecular beacon and T7 exonuclease. With the cycling enzymatic amplification process, this sensor achieved the limit of detection of 1 pM with a good linear correlation in the range of 0-100 pM (R² = 0.9891) using circBART2.2 as a model. Furthermore, we applied the proposed method in the determination of circBART2.2 in cell lysates. The results demonstrated that this method has promising applications in early diagnosis of Epstein-Barr virus (EBV) infection-related diseases using circRNA as the biomarker.

Recent advances in catalytic hairpin assembly signal amplification-based sensing strategies for microRNA detection

Accumulative evidences have indicated that abnormal expression of microRNAs (miRNAs) is closely associated with many health disorders, making them be regarded as potentialbiomarkers for early clinical diagnosis. Therefore, it is extremely necessary to develop a highly sensitive, specific and reliable approach for miRNA analysis. Catalytic hairpin assembly (CHA) signal amplification is an enzyme-free toehold-mediated strand displacement method, exhibiting significant potential in improving the sensitivity of miRNA detection strategies. In this review, we first describe the potential of miRNAs as disease biomarkers and therapeutics, and summarize the latest advances in CHA signal amplification-based sensing strategies for miRNA monitoring. We describe the characteristics and mechanism of CHA signal amplification and classify the CHA-based miRNA sensing strategies into several categories based on the "signal conversion substance", including fluorophores, enzymes, nanomaterials, and nucleotide sequences. Sensing performance, limit of detection, merits and disadvantages of these miRNA sensing strategies are discussed. Moreover, the current challenges and prospects are also presented.

Stimuli-responsive hydrogel microcapsules for the amplified detection of microRNAs

A method for the synthesis of DNA-based acrylamide hydrogel microcapsules loaded with quantum dots as a readout signal is introduced. The shell of DNA-acrylamide hydrogel microcapsules is encoded with microRNA-responsive functionalities, being capable of the detection of cancer-associated microRNA. The microRNA-141 (miR-141), a potential biomarker in prostate cancer, was employed as a model target in the microcapsular biosensor. The sensing principle of the microcapsular biosensor is based on the competitive sequence displacement of target miR-141 with the bridging DNA in the microcapsule's shell, leading to the unlocking of DNA-acrylamide hydrogel microcapsules and the release of the readout signal provided by fluorescent quantum dots. The readout signal is intensified as the concentration of miR-141 increases. While miR-141 was directly measured by DNA-acrylamide hydrogel microcapsules, the linear range for the detection of miR-141 is 2.5 to 50 μM and the limit of detection is 1.69 μM. To improve the sensitivity of the microcapsular biosensor for clinical needs, the isothermal strand displacement polymerization/nicking amplification machinery (SDP/NA) process was coupled to the DNA-acrylamide hydrogel microcapsule sensor for the microRNA detection. The linear range for the detection of miR-141 is improved to the range of 10² to 10⁵ pM and the limit of detection is 44.9 pM. Compared to direct microcapsular biosensing, the detection limit for miR-141 by microcapsules coupled with strand-displacement amplification is enhanced by four orders of magnitude.

Cross-triggered and cascaded recycling amplification system for electrochemical detection of circulating microRNA in human serum

A cross-triggered and cascaded recycling amplification system was developed for electrochemical sensing of microRNA 122 based on the DNAzyme/multicomponent nucleic acid enzyme cleavage technique and a dumbbell-shaped probe. The linear range and detection limit were obtained to be 1 fM-100 pM and 0.34 fM, respectively. Compared with some reported studies, the proposed system can achieve the selective detection of endogenous miRNA in liver injury patients and healthy human serums with the advantages of high sensitivity, low cost, and easy manipulation, which are significant for disease diagnosis as well as the fundamental research of molecular biology.

A fluorescent microarray platform based on catalytic hairpin assembly for MicroRNAs detection

The DNA microarray has distinctive advantages of high-throughput and less complicated operations, but tends to have a relatively low sensitivity. Catalytic hairpin assembly (CHA) is one of the most promising enzyme-free, isothermal DNA circuit for high efficient signal amplification. Here, a microarray-based catalytic hairpin assembly (mi-CHA) biosensing method has been developed to detect various miRNAs in a single test simultaneously. The target miRNA can trigger conformational transformations of hairpin-structured DNA probes on the chip surface and lead to the specific signal amplification. A significant advantage of this approach is that each duplex produced by the solid-phase CHA will be immobilized on the certain location of the chip and release fluorescent signal via the universal domain, eliminating the requirement of different fluorophores. This method has manifested a high detection sensitivity of human cancer-associated miRNAs (miR-21 and miR-155) down to 1.33 fM and promised a high specificity to distinguish single-base mismatches. Furthermore, the practicability of this method was demonstrated by analyzing target miRNAs in human serum and cancer cells. The experimental results suggest that the proposed method has high-throughput analytical potential and could be applied to many other clinical diagnosis.

One-step enzyme-free detection of the miRNA let-7a via twin-stage signal amplification

MicroRNAs (miRNAs) play a significant role in diverse biological processes. The abnormal expression of miRNAs is related to the development of cancers and various diseases. It is of great importance to sensitively and accurately detect miRNAs for early disease diagnosis and treatment. Here, a new fluorescence strategy was initially proposed for the enzyme-free sensing of let-7a by combining the strand displacement reaction (SDR) with the hybridization chain reaction (HCR). The sensor was successfully applied to the detection of the let-7a gene with a wide linear range from 25 pM to 250 nM and a limit of detection (LOD) of 9.01 pM. The fluorescence intensity has a good linear relationship with the logarithm of the target concentration. In addition, the biosensor allowed for the highly sensitive detection of the target genes even in complex human serum samples. With simple operation yet improved detection capability for let-7a, the developed fluorescent biosensor thus shows great potential for early clinical diagnosis as well as biological research.

Dual-Signal Amplification Strategy for Sensitive MicroRNA Detection Based on Rolling Circle Amplification and Enzymatic Repairing Amplification

MicroRNAs (miRNAs) play crucial regulatory roles as post-transcriptional regulators for gene expression and serve as promising biomarkers for diagnosis and prognosis of diseases. Herein, a dual-signal amplification method has been developed for sensitive and selective detection of miRNA based on rolling circle amplification (RCA) and enzymatic repairing amplification (ERA) with low nonspecific background. This strategy designs a padlock probe that can be cyclized in the presence of target miRNA to initiate the RCA reaction, after which the TaqMan probes that are complementary to the RCA products can be cyclically cleaved to produce obvious fluorescence signals with the help of endonuclease IV (Endo IV). Attributed to the dual-signal amplification procedure and the high fidelity of Endo IV, the RCA-ERA method allows quantitative detection of miR-21 in a dynamic range from 2 pM to 5 nM with a low background signal. Moreover, it has the ability to discriminate single-base difference between miRNAs and shows good performance for miRNA detection in complex biological samples. The results demonstrate that the RCA-ERA assay holds a great promise for miRNA-based diagnostics.

A luminescent microRNA nanoprobe based on the target-triggered release of an iridium(III)-solvent complex from mesoporous silica nanoparticles

A luminescent microRNA nanoprobe based on the target-triggered Ir(III)-solvent complex release has been fabricated. The complex is initially embedded into mesoporous silica nanoparticles (MSNs), and then is capped by single-stranded (ss) DNA. In the presence of the target microRNA, the ssDNA hybridize with the microRNA forming a rigid DNA/RNA heteroduplexes and leaving the surface of MSN. Thus, the capped Ir(III) solvent complex is released and re-coordinated with histidine (His) to form a new luminescent complex. The luminescence intensity of the nascent complex (with excitation/emission maxima at 340/570 nm) is positively correlated with the concentrations of the target microRNA in the range from 0.05 to 2 nM, and the detection limit of microRNA is estimated as 0.2 pM (S/N = 3). The ability of this nanoprobe to detect microRNA in cell extract further demonstrates its potential in practical application. Graphical abstractSchematic of a luminescent microRNA nanoprobe based on the target-triggered release of an Ir(III)-solvent complex from mesoporous silica nanoparticles.

Synergy of Peptide-Nucleic Acid and Spherical Nucleic Acid Enabled Quantitative and Specific Detection of Tumor Exosomal MicroRNA

Exosomal microRNAs are essential in intercellular communications and disease progression, yet it remains challenging to quantify the expression level due to their small size and low abundance in blood. Here, we report a "sandwich" electrochemical exosomal microRNA sensor (SEEmiR) to detect target microRNA with high sensitivity and specificity. In SEEmiR, neutrally charged peptide nucleic acid (PNA) enables kinetically favorable hybridization with the microRNA target relative to negatively charged DNA, particularly in a short sequence (10 nt). More importantly, this property allows PNA to cooperate with a spherical nucleic acid (SNA) nanoprobe that heavily loads with oligonucleotide-adsorbed electroactive tags to enhance detection sensitivity and specificity. Such a PNA-microRNA-SNA sandwich construct is able to minimize the background noise via PNA, thereby maximizing the SNA-mediated signal amplification in electrostatic adsorption-based SEEmiR. The synergy between PNA and SNA makes the SEEmiR sensor able to achieve a broad dynamic range (from 100 aM to 1 nM) with a detection limit down to 49 aM (2 orders of magnitude lower than that without SNA) and capable of distinguishing a single-base mismatch. This ultrasensitive sensor provides label-free and enzyme-independent microRNA detection in cell lysates, unpurified tumor exosomal lysates, cancer patients' blood, and accurately differentiates the patients with breast cancer from the healthy ones, suggesting its potential as a promising tool in cancer diagnostics.

A conformational switch-based aptasensor for the chemiluminescence detection of microRNA

A simple microRNA (miRNA) aptasensor has been developed combining the conformational switch of a streptavidin aptamer and isothermal strand displacement amplification. In the presence of its target miRNA, the allosteric molecular beacon (aMB) probe immobilized on the plate can be 'switched on' and release the streptavidin aptamer. At the same time, Klenow fragment (3'→5' exo-) is utilized to initiate DNA-strand displacement, which starts the target recycling process. Based on the aptamer' high binding affinity and subsequent catalytic chemiluminescence (CL) detection, this CL strategy is highly specific in distinguishing mature miRNAs in same family. It exhibits a dynamic range of four orders of magnitude with a detection limit of 50 fM, and shows great potential for miRNA-related clinical practices and biochemical research.

Post-synthesis functionalized hydrogel microparticles for high performance microRNA detection

Encoded hydrogel microparticles, synthesized by Stop Flow Lithography (SFL), have shown great potential for microRNA assays for their capability to provide high multiplexing capacity and solution-like hybridization kinetics. However, due to the low conversion of copolymerization during particle synthesis, current hydrogel microparticles can only utilize ∼10% of the input probes that functionalize the particles for miRNA assay. Here, we present a novel method of functionalizing hydrogel microparticles after particle synthesis by utilizing unconverted double bonds remaining inside the hydrogel particles to maximize functional probe incorporation and increase the performance of miRNA assay. This allows covalent bonding of functional probes to the hydrogel network after particle synthesis. Because of the abundance of the unconverted double bonds and accessibility of all probes, the probe density increases about 8.2 times compared to that of particles functionalized during the synthesis. This results lead to an enhanced miRNA assay performance that improves the limit of detection from 4.9 amol to 1.5 amol. In addition, higher specificity and shorter assay time are achieved compared to the previous method. We also demonstrate a potential application of our particles by performing multiplexed miRNA detections in human plasma samples.

A T7 exonuclease assisted dual-cycle signal amplification assay of miRNA using nanospheres-enhanced fluorescence polarization

Based on streptavidin coated nanospheres and T7 exonuclease assisted dual-cycle signal amplification, we developed a novel sensitive fluorescence polarization detection method for miRNA. When target miRNA was present in the system, hairpin probe hybridized with miRNA, forming a double-stranded structure. The 5' end of hairpin probe was then recognized and digested by T7 exonuclease, releasing the non-degraded single strand DNA fragments and miRNA. The released target miRNA could trigger the next cycle of hybridization and digestion, releasing more non-degraded fragments from hairpin probe. The fragments could hybridize with a signal probe (with carboxyfluorescein modification at 5'-end and biotin modification at 3'-end). The formed blunt 5'-end of signal probe was then recognized and degraded by T7 exonuclease, releasing the fragments and the fluorophore carboxyfluorescein. The next cycle of hybridization and digestion of signal probe was triggered by the released fragment at the same time. The free carboxyfluorescein cannot connect with streptavidin coated nanospheres which were used as the fluorescence polarization signal amplifier. So, there was a big change of fluorescence polarization signal after adding miRNA into the detection system, due to the different fluorescence polarization signal between nanospheres-captured intact signal probe and free carboxyfluorescein. The detection limit of this method is about 0.001 nM, and it has a good selectivity. In addition, it was also applicable to determine target miRNA in total miRNA extracts and compare the expression level of target miRNA in different cells. Consequently, the proposed method is expected to be used for the potential cancer diagnosis and the related biomedical research.

Functional MoS2 nanosheets for precursor and mature microRNA detection in living cells

Mature microRNAs (miRNAs) are small-sized RNAs cleaved from precursor microRNAs (pre-miRNAs) by the RNase Dicer. Various miRNAs play key regulatory roles in tumorigenesis and metastasis, and are therefore potential diagnostic and prognostic cancer biomarkers. However, detecting miRNAs and pre-miRNAs accurately and selectively in living cells remains a major challenge, as the mature miRNA sequence is also present in its pre-miRNA and current sequence probes exhibit poor gene delivery efficiency. Herein, we report a strategy for selectively and accurately detecting miRNA-21 and pre-miRNA-21 in living cells using functional MoS₂ nanosheets (NSs) loaded with rationally engineered molecular beacons (MBs). The exfoliated MoS₂ nanosheets (NSs) with a mean lateral diameter of 50-70 nm were functionalized with the aptamer AS1411 and polyethylene glycol (MoS₂-PEG-AS) to achieve target-cell-specific delivery and to enhance biocompatibility. The large available surface of the MoS₂-PEG-AS was loaded with MB probes. The resulting MoS₂-PEG-AS/MBs present cancer-cell-targeting ability, good protection properties, good optical stability, and biocompatibility. We demonstrated that the resulting nanoprobes can selectively image miRNA-21 and pre-miRNA-21 in various cell lines by facilitating enhanced fluorescence in the presence of miRNA-21 and pre-miRNA-21. Thus, these MoS₂-PEG-AS/MBs are potentially a tool to discriminate between intracellular miRNA and pre-miRNA at different expression levels. Graphical abstract.

Cascade Transcription Amplification of RNA Aptamer for Ultrasensitive MicroRNA Detection

MicroRNAs (miRNAs) play a critical role in multifarious biological processes and being deemed to be important biomarkers for clinical cancer diagnosis, prognosis, and therapy. Thus, assays for sensitive and accurate quantification of miRNAs are highly demanded. Herein, we have constructed a RNA aptamer involved cascade transcription amplification method (termed RACTA), enabling label-free, ultrasensitive, and specific detection of miRNA. Target miRNA-initiated strand-displacement amplification would allow for the production of plenty of ssDNA that triggers the subsequent transcriptional amplification of spinach RNA aptamers. Consequently, transcribed tremendous spinach aptamers activated fluorophore DFHBI (( Z)-4-(3,5-difluoro-4-hydroxybenzylidene)-1,2-dimethyl-1 H-imidazol-5(4 H)-one) for miRNA quantitative analysis. RACTA outperforms conventional strand displacement amplification (SDA) at both background and amplification rate due to the light-up mechanism of DFHBI dye-Spinach aptamer and cascade signal amplification of RACTA. Thus, the signal-to-noise ratio of RACTA was increased by about 20-fold compared to that of SDA. This RACTA assay could confer a highly sensitive detection of miRNA with a detection limit of 5.12 × 10^-18 M and excellent specificity enabling differentiation between miRNAs and homologous families. Besides, this assay has been successfully demonstrated for quantification of miRNAs in different cell lines. Therefore, the proposed method holds great potential for miRNA biomarker based early diagnosis and prognosis monitoring.

Quantitative and Specific Detection of Exosomal miRNAs for Accurate Diagnosis of Breast Cancer Using a Surface-Enhanced Raman Scattering Sensor Based on Plasmonic Head-Flocked Gold Nanopillars

MicroRNAs in exosomes (exosomal miRNAs) have attracted increased attention as cancer biomarkers for early diagnosis and prognosis owing to their stability in body fluids. Since strong association exists between exosomal miRNA expression levels and breast cancer, the development of effective methods that can monitor exosomal miRNA expression both over broad concentration ranges and in ultralow amounts is critical. Here, a surface-enhanced Raman scattering (SERS)-based sensing platform is developed for the quantitative determination of exosomal miRNAs. Ultrasensitive exosomal miRNA detection with single-nucleotide specificity is obtained from enhanced SERS signals from a uniform plasmonic head-flocked gold nanopillar substrate, which generates multiple hotspots and enables hybridization between short oligonucleotides, i.e., miRNAs and locked nucleic acid probes. The proposed SERS sensor shows an extremely low detection limit without any amplification process, a wide dynamic range (1 am to 100 nm), multiplex sensing capability and sound miRNA recovery in serum. Furthermore, this sensor allows reliable observation of exosomal miRNA expression patterns from breast cancer cell lines and can discriminate breast cancer subtype based on the difference between these patterns. The results suggest that this sensor can be used for universal cancer diagnosis and further biomedical applications through the quantitative measurement of exosomal miRNAs in bodily fluids.

The role of gene sculptor microRNAs in human precancerous lesions

MicroRNAs (miRNAs) are small noncoding RNAs. These noncoding RNAs regulate the expression of target genes and inhibit the translation of target proteins at the post-transcriptional level. miRNAs also play an important role in human health, from the development and differentiation of cells to the occurrence and progression of disorders such as cancer, cardiovascular diseases, and neurodegenerative diseases. Precancerous lesions are lesions prior to invasive carcinomas, and carcinogenesis is a very complicated process, which is multistage and the result of multigene synergy. miRNAs exert effects as both oncogenes and tumor suppressor genes by regulating target genes involved in signaling pathways. Hence, precancerous lesions are accompanied by relevant miRNA changes. Based on the morphology of miRNAs in vivo and the specificity of miRNA, various novel miRNA analysis methods have been developed, including reverse transcription quantitative PCR, enzyme analysis, molecular beacons, and deep sequencing. For example, in the laryngeal epithelial precancerous lesions, the data demonstrate that the expression of miR-10a-5p is downregulated and miR-484 is the most abundant miRNA in hepatic precancerous lesions. In this review, we discuss the functional roles of miRNAs in human precancerous lesions.

Upconversion nanocrystal 'armoured' silica fibres with superior photoluminescence for miRNA detection

We have fabricated a flexible membrane, consisting of SiO2 nanofibres armoured with upconversion nanoparticles, exhibiting intense photoluminescence. These assemblies were subsequently grafted with molecular beacons to produce a biosensor suitable for the detection of specific microRNA and with applications in early cancer detection and point-of-care diagnosis.

Nicking-enhanced rolling circle amplification for sensitive fluorescent detection of cancer-related microRNAs

In this study, a biosensing system based on nicking-enhanced rolling circle amplification (N-RCA) was proposed for the highly sensitive detection of cancer-related let-7a microRNA (miRNA). The sensing system consists of a padlock probe (PP), which contains a target recognition sequence and two binding sites for nicking endonuclease (NEase), and molecular beacon (MB) as reporting molecule. Upon hybridization with let-7a, the PP can be circularized by ligase. Then, the miRNA acted as polymerization primer to initiate rolling circle amplification (RCA). With the assistance of NEase, RCA products can be nicked on the cyclized PP and are displaced during the subsequent duplication process, generating numerous nicked fragments (NFs). These NFs not only induce another RCA reaction but also open the molecular beacons (MBs) via hybridization, leading to significantly amplified fluorescence signal. Under the optimized conditions, this method exhibits high sensitivity toward target miRNA let-7a with a detection limit of as low as 10 pM, a dynamic range of three orders of magnitude is achieved, and its family member is easily distinguished even with only one mismatched base. Meanwhile, it displays good recovery and satisfactory reproducibility in fetal bovine serum (FBS). Therefore, these merits endow the newly proposed N-RCA strategy with powerful implications for miRNA detection. Graphical abstract A biosensing system based on nicking-enhanced rolling circle amplification (N-RCA) for the highly sensitive detection of cancer-related let-7a microRNA.

Fluorometric determination of microRNA-155 in cancer cells based on carbon dots and MnO2 nanosheets as a donor-acceptor pair

A fluorometric method is presented for sensitive deternination of microRNA. It is making use of carbon dots (C-dots) loaded with a DNA probe as fluorophore and MnO₂ nanosheets as the quenching agent. The blue-green fluorescence of the DNA-loaded C-dots is quenched by the MnO₂ nanosheets, but restored on binding target microRNA-155. The maximum excitation wavelength and the maximum emission wavelength of C-dots are at 360 nm and 455 nm, respectively. Fluorescence correlates linearly with the log of the microRNA-155 concentration in two ranges, viz. from 0.15 to 1.65 aM and from 1.65 to 20 aM. The detection limit is as low as 0.1 aM. The assay can discriminate between fully complementary and single-base mismatch microRNA. The assay displayed high specificity when used to detect MCF-7 breast cancer cells which can be detected in concentrations from 1000 to 45,000 cells·mL^-1, with a 600 cells·mL^-1 detection limit. The method was applied to the analysis of serum samples spiked with microRNA, and satisfactory results were acquired. Graphical abstract Schematic of a fluorometric sensing platform for miRNA-155. The method relies on a FRET process between C-dots and MnO₂ nanosheets. This strategy has a practical application for detection of miRNA in cell lines and biological fluids.

High-Discrimination Factor Nanosensor Based on Tetrahedral DNA Nanostructures and Gold Nanoparticles for Detection of MiRNA-21 in Live Cells

While detection of microRNA with or without signal amplification is highly informative, nanosensors with high specificity for cell-specific RNA detection are rare. Methods: In this study, a tetrahedral DNA nanostructure (TDN) with a specific function was combined with gold nanoparticles (Au-NP) possessing fluorescence quenching effects and a large surface area to fabricate a fluorescence resonance energy transfer based nanosensor (Au-TDNN). The presence of miR-21 (target) can separate the fluorescent dye-labeled detection probe on Au-TDNNs from Au-NPs, which separates the donor and acceptor, thus inducing an intensive fluorescence signal. High specificity for discerning point mutation targets was achieved by rationally designing the nucleic acid strand displacement reaction to occur spontaneously with ΔG⁰ ≈ 0 based on thermodynamic parameters; under this condition, slight thermodynamic changes caused by base mismatch exert significant effects on hybridization yield. Results: Chemically synthesized DNA of three single-base-changed analogues of target, let-7d, and miR-200b were tested. A discrimination factor (DF) of 15.4 was produced by the expected detection probe on Au-NPs for proximal single-base mismatch. As the control group, the DF produced by an ordinary detection probe on Au-NPs only reached 2.4. The feasibility of the proposed strategy was also confirmed using hepatocyte cancer cells (HepG2). Conclusion: This improved nanosensor opens a new avenue for the specific and easy detection of microRNA in live cells.

An ultrasensitive detection of miRNA-155 in breast cancer via direct hybridization assay using two-dimensional molybdenum disulfide field-effect transistor biosensor

MicroRNAs (miRNAs), critical biomarkers of acute and chronic diseases, play key regulatory roles in many biological processes. As a result, robust assay platforms to enable an accurate and efficient detection of low-level miRNAs in complex biological samples are of great significance. In this work, a label-free and direct hybridization assay using molybdenum disulfide (MoS₂) field-effect transistor (FET) biosensor has been developed for ultrasensitive detection of miRNA-155 as a breast cancer biomarker in human serum and cell-line samples. MoS₂, the novel 2D layered material with excellent physical and chemical properties, was prepared through sequential solvent exchange method and was used as an active channel material. MoS₂ was comprehensively characterized by spectroscopic and microscopic methods and it was applied for fabrication of FET device by drop-casting MoS₂ flacks suspension onto the FET surface. MoS₂ FET device showed a relatively low subthreshold swing of 48.10mV/decade and a high mobility of 1.98 × 10³cm²V^-1s^-1. Subsequently, probe miRNA-155 strands were immobilized on the surface of the MoS₂ FET device. Under optimized conditions detection limit of 0.03fM and concentration range 0.1fM to 10nM were achieved. The developed biosensor not only was capable to identification of fully matched versus one-base mismatch miRNA-155 sequence, but also it could detect target miRNA-155 in spiked real human serum and extracts from human breast cancer cell-line samples. This approach paves a way for label-free, early detection of miRNA as a biomarker in cancer diagnostics with very high sensitivity and good specificity, thus offering a significant potential for clinical application.

Attomolar detection of extracellular microRNAs released from living prostate cancer cells by a plasmonic nanowire interstice sensor

Prostate cancer (PC) is the second leading cause of cancer death for men worldwide. The serum prostate-specific antigen level test has been widely used to screen for PC. This method, however, exhibits a high false-positive rate, leading to over-diagnosis and over-treatment of PC patients. Extracellular microRNAs (miRNAs) recently provided valuable information including the site and the status of the cancers and thus emerged as new biomarkers for several cancers. Among them, miR141 and miR375 are the most pronounced biomarkers for the diagnosis of high-risk PC. Herein, we report an attomolar detection of miR141 and miR375 released from living PC cells by using a plasmonic nanowire interstice (PNI) sensor. This sensor showed a very low detection limit of 100 aM as well as a wide dynamic range from 100 aM to 100 pM for all target miRNAs. In addition, the PNI sensor could discriminate perfectly the diverse single-base mismatches in the miRNAs. More importantly, the PNI sensor successfully detected the extracellular miR141 and miR375 released from living PC cell lines (LNCaP and PC-3), proving the diagnostic ability of the sensor for PC. We anticipate that the present PNI sensor can hold great promise for the precise diagnosis and prognosis of various cancer patients as well as PC patients.

Digital direct detection of microRNAs using single molecule arrays

MicroRNAs (miRNAs) are involved in many biological pathways, and detecting miRNAs accurately is critical for diagnosing a variety of diseases including cancer. However, most current methods for miRNA detection require lengthy sample preparation and amplification steps that can bias the results. In addition, lack of specificity and reproducibility give rise to various challenges in detection of circulating miRNAs in biological samples. In this work, we applied the Single Molecule Array (Simoa) technique to develop an ultra-sensitive sandwich assay for direct detection of multiple miRNAs without pre-amplification. We successfully detected miRNAs at femtomolar concentrations (with limits of detection [LODs] ranging from 1 to 30 fM) and high specificity (distinguishing miRNAs with a single nucleotide mismatch). This method was effective against a range of diverse target sequences, suggesting a general approach for miRNA detection. To demonstrate the practical application of this technique, we detected miRNAs in a variety of sample types including human serum and total RNA. The high sensitivity and simple workflow of the Simoa method represent excellent advantages for miRNA-based diagnostics of human diseases.