Precise Quantitation of MicroRNA in a Single Cell with Droplet Digital PCR Based on Ligation Reaction

Multiplex digital PCR for the simultaneous quantification of a miRNA panel

BACKGROUND

microRNAs (miRNAs) are small non-coding RNAs regulating gene expression. They have attracted significant interest as biomarkers for early diagnosis, prediction and monitoring of treatment response in many diseases. As individual miRNAs often lack the required sensitivity and specificity, miRNA signatures are developed for clinical applications. Digital PCR (dPCR) is a sensitive fluorescent-based quantification method, that can be used to detect the expression of miRNAs in patient samples. Our study presents the first proof-of-concept of a multiplexed dPCR assay for the simultaneous analysis and quantification of multiple miRNAs.

RESULTS

After reverse transcription (RT) using a pool of miRNA-specific stem-loop primers, dPCR was performed with a universal reverse primer and miRNA-specific forward primers along with fluorescently-labelled hydrolysis probes. Multiple experimental parameters were evaluated and strategies for modulating the observed signals were devised. The optimised assay was applied to the analysis of miRNAs from cell lines and biological samples. Although absolute quantification was lost, due to the reverse transcription step, quantification was linear for the dilution series and results were highly reproducible for independent dPCR and RT reactions. Our results confirmed the high sensitivity of dPCR for patient samples.

CONCLUSIONS

We demonstrate the feasibility and reliability of multiplexed detection and quantification of miRNAs by dPCR that can be applied in a clinical setting to evaluate miRNA signatures.

Single-Cell Multiplexed Signal Amplification Strategy Based on Catalytic Hairpin Self-Assembly and CRISPR/Cas12a for Exploring the Relationship between lncRNA HOTAIR and miRNA-122 in Individual Hepatocytes

The long noncoding RNA (lncRNA) HOTAIR has been shown to act as an oncogene in a variety of cancers, including hepatocellular carcinoma (HCC). MicroRNA-122 (miR-122) is a key liver-specific miRNA that is frequently inhibited in HCC and is associated with poor prognosis. However, a potential relationship between HOTAIR and miR-122 in individual hepatocytes has not been explored. To this end, we propose here an intracellular catalytic hairpin self-assembly-CRISPR/Cas12a tandem multiplexed signal amplification strategy for the simultaneous quantification of HOTAIR and miRNA-122 in a single hepatocyte. We applied this method to analyze both normal HL-7702 liver cells and HepG2 HCC cells, and found that HL-7702 cells contained large amounts of miRNA-122, while the content of miRNA-122 in HepG2 cells was low. However, the level of HOTAIR in HepG2 cells was much higher than that in HL-7702 cells, confirming the overexpression of HOTAIR in HCC cells. We achieved the simultaneous absolute quantification of HOTAIR and miRNA-122 in single cells, providing an important method to study the relationships between these two RNA molecules in individual cells.

Quantitative Analysis of Cell-Free RNA at Attomolar Level Using CRISPR/Cas Digital Imaging Platform

Quantitative analysis of cell-free RNA (cfRNA) in plasma sample can be used for screening, diagnosing, and prognosticating of multiple diseases. Here, we report a quantitative CRISPR/Cas digital imaging platform (qCasdip) for the detection of various cfRNAs, including circular RNAs and miRNAs, in clinical samples at the attomolar (aM) level without the need for preamplification. Digital counting strategy provides qCasdip quantitative ability with a linear detection range of 102-106 aM. Meanwhile, qCasdip demonstrated cfRNA profiling in clinical plasma samples, improving the diagnosis of breast cancer. These data highlight the potential of qCasdip to quantitatively assess the molecular patterns of specific cfRNA panels in plasma, thereby providing a novel liquid biopsy solution to enhance disease diagnosis.

Click chemical ligation-enabled digital particle counting for multiplexed microRNA analysis

Digital counting assays, that quantify targets by counting individual signal entities, provide a promising way for the sensitive analysis of biomarkers even at the single-molecule level. Considering the requirements of complex enzyme-catalyzed amplification techniques and specialized instruments in traditional digital counting biosensors, herein, a simple digital counting platform for microRNA (miRNA) analysis is developed by employing the miRNA-templated click chemical ligation to hinge ultrabright quantum dot-doped nanoparticles (QDNPs) on the bottom of microplate well. Compared with the traditional short miRNA-mediated sandwich hybridization mechanism, the click chemistry-mediated ligation featured enhanced stability, achieving higher sensitivity by directly counting the number of QDNPs with a common wide-field fluorescence microscope. Furthermore, enzyme-free cycling click ligation strategy is adopted to push the detection limit of miRNA down to a low level of 8 fM. What is more, taking advantages of the tunable emission wavelength and narrow emission spectra of fluorescent nanoparticles, the platform enables simultaneous detection of multiplex miRNA targets without cross interference. Benefiting from the simple operation, high sensitivity, and good generality, miRNA analysis in complex samples is successfully achieved. This method not only pioneers a new route for digital counting assays but also holds great potential in miRNA-related biological researches.

Ultrasensitive Electrochemiluminescence Imaging Detection of Multiple miRNAs in Single Cells with a Closed Bipolar Electrode Array Chip

In situ sensitive detection of multiple biomarkers in a single cell was highly necessary for understanding the pathogenesis mechanism and facilitating disease diagnosis. Herein, a bipolar electrode (BPE)-electrochemiluminescence (ECL) imaging chip was designed for ultrasensitive in situ detection of multiple miRNAs in single cells based on a dual-signal amplification strategy. A single cell was trapped and lysed within the microtrap of the cathode chamber and an HCR amplification process and nanoprobes (Fc/DNA/Fe3O4) were introduced, leading to a large number of electroactive molecules (Fc) being modified on the surface. Under a suitable potential, Fc+ in the cathodic chamber was reduced to Fc and L-012 was oxidized in the anodic chamber according to the electric neutrality principle of the bipolar electrode system, resulting in the ECL signal recorded by EMCCD. Ascribed to the dual-signal amplification, sensitive visual detection of miRNA-21 and miRNA-155 in single cells was achieved. For MCF-7 cells, miRNA-21 and miRNA-155 were calculated to be 4385 and 1932 copies/cell (median), respectively. For HeLa cells, miRNA-21 and miRNA-155 were calculated to be 1843 and 1012 copies/cell (median), respectively. The comprehensive evaluation of two kinds of miRNA could effectively eliminate error signals, and the detection precision was improved by 10%.

Integrated Droplet-Based Digital Loop-Mediated Isothermal Amplification Microfluidic Chip with Droplet Generation, Incubation, and Continuous Fluorescence Detection

This study integrated sample partition, incubation, and continuous fluorescence detection on a single microfluidic chip for droplet-based digital Loop-Mediated Isothermal Amplification (LAMP) of nucleic acids. This integration eliminated the need to transfer reactions between different platforms, avoiding sample contamination and loss. Prior to the reaction, filling the channels with an oil phase and adding a glass cover slip on top of the chip overcame the problem of bubble generation in the channels during the LAMP reaction due to heating. Additionally, using two fluorescence intensity thresholds enabled simultaneous detection and counting of positive and negative droplets within a single fluorescence detection channel. The chip can partition approximately 6000 droplets from a 5 µL sample within 10 min, with a droplet diameter of around 110 µm and a coefficient of variation (CV) value of 0.82%. Staphylococcus aureus was quantified via the proposed platform. The results demonstrated a highly accurate correlation coefficient (R = 0.9998), and the detection limit reached a concentration of 1.7 × 102 copies/µL. The entire process of the droplet digital LAMP reaction, from droplet generation to incubation to quantitative results, took a maximum of 70 min.

Discrimination of Multiple Homologous Sequences Based on DNA Logic Gate and Elemental Labeling Technology

The simultaneous discrimination of multiple homologous sequences faces challenges due to the high similarity of sequences and the complexity of the discrimination system in most reported works. Herein, a simple and ingenious analysis method was developed to identify eight miRNAs of the let-7 family by combining logic gates and entropy-driven catalytic (EDC)-based lanthanide labeling inductively coupled plasma mass spectrometry (ICP-MS) technology. Specifically, eight miRNAs were first divided into four types according to the difference of bases in the domains 2 and 3 on sequences. To identify the type of targets, a DNA logic gate was constructed with two strand displacement reactions on magnetic beads that could be initiated by different types of targets. Based on the difference of the output signals after two strand displacement reactions, the type of targets was distinguished preliminarily. Then, the discrimination of a specific target was achieved with EDC-based lanthanide labeling ICP-MS detection. By labeling the different magnetic probes with different elemental tags, a specific element signal released from magnetic beads after EDC could be detected by ICP-MS, and therefore, simultaneous detection of homologous sequences was completed. This work provided a novel and simple method for highly specific identification of homologous sequences with the assistance of a logic gate and can promote further development of elemental labeling ICP-MS in the field of multiple analysis.

Digital PCR for Single-Cell Analysis

Single-cell analysis provides an overwhelming strategy for revealing cellular heterogeneity and new perspectives for understanding the biological function and disease mechanism. Moreover, it promotes the basic and clinical research in many fields at a single-cell resolution. A digital polymerase chain reaction (dPCR) is an absolute quantitative analysis technology with high sensitivity and precision for DNA/RNA or protein. With the development of microfluidic technology, digital PCR has been used to achieve absolute quantification of single-cell gene expression and single-cell proteins. For single-cell specific-gene or -protein detection, digital PCR has shown great advantages. So, this review will introduce the significance and process of single-cell analysis, including single-cell isolation, single-cell lysis, and single-cell detection methods, mainly focusing on the microfluidic single-cell digital PCR technology and its biological application at a single-cell level. The challenges and opportunities for the development of single-cell digital PCR are also discussed.

A one-pot isothermal Cas12-based assay for the sensitive detection of microRNAs

The use of microRNAs as clinical cancer biomarkers is hindered by the absence of accurate, fast and inexpensive assays for their detection in biofluids. Here we report a one-step and one-pot isothermal assay that leverages rolling-circle amplification and the endonuclease Cas12a for the accurate detection of specific miRNAs. The assay exploits the cis-cleavage activity of Cas12a to enable exponential rolling-circle amplification of target sequences and its trans-cleavage activity for their detection and for signal amplification. In plasma from patients with pancreatic ductal adenocarcinoma, the assay detected the miRNAs miR-21, miR-196a, miR-451a and miR-1246 in extracellular vesicles at single-digit femtomolar concentrations with single-nucleotide specificity. The assay is rapid (sample-to-answer times ranged from 20 min to 3 h), does not require specialized instrumentation and is compatible with a smartphone-based fluorescence detection and with the lateral-flow format for visual readouts. Simple assays for the detection of miRNAs in blood may aid the development of miRNAs as biomarkers for the diagnosis and prognosis of cancers.

Single-microbead space-confined digital quantification strategy (SMSDQ) for counting microRNAs at the single-molecule level

Quantification of microRNAs (miRNAs) at the single-molecule level is of great significance for clinical diagnostics and biomedical research. The challenges lie in the limits to transforming single-molecule measurements into quantitative signals. To address these limits, here, we report a new approach called a Single Microbead-based Space-confined Digital Quantification (SMSDQ) to measure individual miRNA molecules by counting gold nanoparticles (AuNPs) with localized surface plasmon resonance (LSPR) light-scattering imaging. One miRNA target hybridizes with the alkynyl-modified capture DNA probe immobilized on a microbead (60 μm) and the azide-modified report DNA probe anchored on AuNP (50 nm), respectively. Through the click reaction between the alkynyl and azide group, a single microbead can covalently link the AuNPs in the confined space within the view of the microscope. By digitally counting the light-scattering spots of AuNPs, we demonstrated the proposed approach with single-molecule detection sensitivity and high specificity of single-base discrimination. Taking the advantages of ultrahigh sensitivity, specificity, and the digital detection manner, the approach is suitable for evaluating cell heterogeneity and small variations of miRNA expression and has been successfully applied to direct quantification of miRNAs in one-tenth single-cell lysates and serum samples without RNA-isolated and nucleic acid amplification steps.

Peroxidase-mimicking poly-L-lysine/alginate microspheres with PtS2 nanoparticles for image-based colorimetric assays

Morphologically controllable ALG@ε-PL water-in-water microspheres were successfully prepared using a two-step method through precise control of the two-phase flow rate. Through further interfacial coagulation, the ALG@ε-PL microspheres possess a dense surface structure and good permeability. The sensor based on PtS₂@ALG@ε-PL microspheres was constructed by encapsulating PtS₂ nanosheets with peroxidase-like properties in ALG@ε-PL water-in-water microspheres. PtS₂ nanosheets catalyze the oxidation of 3,3',5,5'-tetramethylbenzidine (TMB) by H₂O₂ to produce blue oxTMB. The strong reducing property of the model analyte dopamine (DA) can reduce oxTMB, thus causing the blue color to fade and successfully achieving colorimetric detection of DA. The linear range of the assay is 2.0-200 μM, and the detection limit is 0.22 μM. The recoveries of DA in serum samples were determined by the spik method, and the results were reproducible.

Single cell quantification of microRNA from small numbers of non-invasively sampled primary human cells

Expression levels of microRNAs (miRNAs) in single cells are low and conventional miRNA detection methods require amplification that can be complex, time-consuming, costly and may bias results. Single cell microfluidic platforms have been developed; however, current approaches are unable to absolutely quantify single miRNA molecules expressed in single cells. Herein, we present an amplification-free sandwich hybridisation assay to detect single miRNA molecules in single cells using a microfluidic platform that optically traps and lyses individual cells. Absolute quantification of miR-21 and miR-34a molecules was achieved at a single cell level in human cell lines and validated using real-time qPCR. The sensitivity of the assay was demonstrated by quantifying single miRNA molecules in nasal epithelial cells and CD3⁺ T-cells, as well as nasal fluid collected non-invasively from healthy individuals. This platform requires ~50 cells or ~30 µL biofluid and can be extended for other miRNA targets therefore it could monitor miRNA levels in disease progression or clinical studies.

An electrochemical determination strategy for miRNA based on bimetallic nanozyme and toehold-mediated DNA replacement procedure

An electrochemical strategy based on bimetallic nanozyme in collaboration with toehold-mediated DNA replacement effect is proposed for the sensitive determination of miRNA-21. The AuPt nanoparticles (AuPt NPs) are prepared as a catalytic beacon; it shows favorable peroxidase properties with a Michaelis contant (K_m) of 0.072 mM for H₂O₂, which is capable of catalyzing H₂O₂ to induce an intense redox reaction, and causing a measurable electrochemical signal. To further enhance the strength of the signal response, a novel toehold-mediated DNA replacement strategy is employed. DNA strands with specific sequences are modified on electrodes and AuPt NPs, respectively. In the presence of miRNA-21, a cyclic substitution effect is subsequently activated via a specific toehold sequence and leads to a large accumulation of AuPt NPs on the electrodes. Subsequently, a strong signal depending on the amount of miRNA-21 is obtained after adding a small amount of H₂O₂. The analytical range of this determination method is from 0.1 pM to 1.0 nM, and the LOD is 84.1 fM. The spike recoveries for serum samples are 95.0 to 102.4% and the RSD values are 3.7 to 5.8%. The results suggests a promising application of the established method in clinical testing and disease diagnosis.

A Short Review on Miniaturized Biosensors for the Detection of Nucleic Acid Biomarkers

Even today, most biomarker testing is executed in centralized, dedicated laboratories using bulky instruments, automated analyzers, and increased analysis time and expenses. The development of miniaturized, faster, low-cost microdevices is immensely anticipated for substituting for these conventional laboratory-oriented assays and transferring diagnostic results directly onto the patient's smartphone using a cloud server. Pioneering biosensor-based approaches might make it possible to test biomarkers with reliability in a decentralized setting, but there are still a number of issues and restrictions that must be resolved before the development and use of several biosensors for the proper understanding of the measured biomarkers of numerous bioanalytes such as DNA, RNA, urine, and blood. One of the most promising processes to address some of the issues relating to the growing demand for susceptible, quick, and affordable analysis techniques in medical diagnostics is the creation of biosensors. This article critically discusses a short review of biosensors used for detecting nucleic acid biomarkers, and their use in biomedical prognostics will be addressed while considering several essential characteristics.

Advances in droplet digital polymerase chain reaction on microfluidic chips

The PCR technique has been known to the general public since the pandemic outbreak of COVID-19. This technique has progressed through three stages: from simple PCR to real-time fluorescence PCR to digital PCR. Among them, the microfluidic-based droplet digital PCR technique has attracted much attention and has been widely applied due to its advantages of high throughput, high sensitivity, low reagent consumption, low cross-contamination, and absolute quantification ability. In this review, we introduce various designs of microfluidic-based ddPCR developed within the last decade. The microfluidic-based droplet generation methods, thermal cycle strategies, and signal counting approaches are described, and the applications in the fields of single-cell analysis, disease diagnosis, and pathogen detection are introduced. Further, the challenges and prospects of microfluidic-based ddPCR are discussed. We hope that this review can contribute to the further development of the microfluidic-based ddPCR technique.

Droplet microfluidics for CTC-based liquid biopsy: a review

Circulating tumor cells (CTCs) are important biomarkers of liquid biopsy. The number and heterogeneity of CTCs play an important role in cancer diagnosis and personalized medicine. However, owing to the low-abundance biomarkers of CTCs, conventional assays are only able to detect CTCs at the population level. Therefore, there is a pressing need for a highly sensitive method to analyze CTCs at the single-cell level. As an important branch of microfluidics, droplet microfluidics is a high-throughput and sensitive single-cell analysis platform for the quantitative detection and heterogeneity analysis of CTCs. In this review, we focus on the quantitative detection and heterogeneity analysis of CTCs using droplet microfluidics. Technologies that enable droplet microfluidics, particularly high-throughput droplet generation and high-efficiency droplet manipulation, are first discussed. Then, recent advances in detecting and analyzing CTCs using droplet microfluidics from the different aspects of nucleic acids, proteins, and metabolites are introduced. The purpose of this review is to provide guidance for the continued study of droplet microfluidics for CTC-based liquid biopsy.

Non-coding RNAs in immunoregulation and autoimmunity: Technological advances and critical limitations

Immune cell function is critically dependent on precise control over transcriptional output from the genome. In this respect, integration of environmental signals that regulate gene expression, specifically by transcription factors, enhancer DNA elements, genome topography and non-coding RNAs (ncRNAs), are key components. The first three have been extensively investigated. Even though non-coding RNAs represent the vast majority of cellular RNA species, this class of RNA remains historically understudied. This is partly because of a lag in technological and bioinformatic innovations specifically capable of identifying and accurately measuring their expression. Nevertheless, recent progress in this domain has enabled a profusion of publications identifying novel sub-types of ncRNAs and studies directly addressing the function of ncRNAs in human health and disease. Many ncRNAs, including circular and enhancer RNAs, have now been demonstrated to play key functions in the regulation of immune cells and to show associations with immune-mediated diseases. Some ncRNAs may function as biomarkers of disease, aiding in diagnostics and in estimating response to treatment, while others may play a direct role in the pathogenesis of disease. Importantly, some are relatively stable and are amenable to therapeutic targeting, for example through gene therapy. Here, we provide an overview of ncRNAs and review technological advances that enable their study and hold substantial promise for the future. We provide context-specific examples by examining the associations of ncRNAs with four prototypical human autoimmune diseases, specifically rheumatoid arthritis, psoriasis, inflammatory bowel disease and multiple sclerosis. We anticipate that the utility and mechanistic roles of these ncRNAs in autoimmunity will be further elucidated in the near future.

Partitioning and subsampling statistics in compartment-based quantification methods

The precision of compartment-based quantification methods is subject to multiple effects, of which partitioning and subsampling play a major role. Partitioning is the process of aliquoting the sample liquid and consequently the contained target molecules, whereas subsampling denotes the fact that usually only a portion of a sample is analyzed. In this work, we present a detailed statistical description comprising the effects of partitioning and subsampling on the relative uncertainty of the test result. We show that the state-of-the-art binomial model does not provide accurate results for the level of subsampling present when analyzing the nucleic acid content of single specific cells. Hence, in this work we address partitioning and subsampling effects separately and subsequently combine them to derive the relative uncertainty of a test system and compare it for single cell content analysis and body fluid analysis. In point-of-care test systems the area for partitioning and detection is usually limited, which means that a trade-off between the number of partitions (related to a partitioning uncertainty) and the amount of analyzed volume (related to a subsampling uncertainty) might be inevitable. In case of low target concentration, the subsampling uncertainty is dominant whereas for high target concentration, the partitioning uncertainty increases, and a larger number of partitions is beneficial to minimize the combined uncertainty. We show, that by minimizing the subsampling uncertainty in the test system, the quantification uncertainty of low target concentrations in single cell content analysis is much smaller than in body fluid analysis. In summary, the work provides the methodological basis for a profound statistical evaluation of partitioning and subsampling effects in compartment-based quantification methods and paves the way towards an improved design of future digital quantification devices for highly accurate molecular diagnostic analysis at the point-of-care.

Advances in optical counting and imaging of micro/nano single-entity reactors for biomolecular analysis

Ultrasensitive detection of biomarkers is of paramount importance in various fields. Superior to the conventional ensemble measurement-based assays, single-entity assays, especially single-entity detection-based digital assays, not only can reach ultrahigh sensitivity, but also possess the potential to examine the heterogeneities among the individual target molecules within a population. In this review, we summarized the current biomolecular analysis methods that based on optical counting and imaging of the micro/nano-sized single entities that act as the individual reactors (e.g., micro-/nanoparticles, microemulsions, and microwells). We categorize the corresponding techniques as analog and digital single-entity assays and provide detailed information such as the design principles, the analytical performance, and their implementation in biomarker analysis in this work. We have also set critical comments on each technique from these aspects. At last, we reflect on the advantages and limitations of the optical single-entity counting and imaging methods for biomolecular assay and highlight future opportunities in this field.

Single-Cell Analysis of circRNA Using ddPCR

Droplet digital polymerase chain reaction (ddPCR) is a new quantitative PCR method based on water-oil emulsion droplet technology. ddPCR enables highly sensitive and accurate quantification of nucleic acid molecules, especially when their copy numbers are low. In ddPCR, a sample is fractionated into ~20,000 droplets, and every nanoliter-sized droplet undergoes PCR amplification of the target molecule. The fluorescence signals of droplets are then recorded by an automated droplet reader. Circular RNAs (circRNAs) are single-stranded, covalently closed RNA molecules that are ubiquitously expressed in animals and plants. CircRNAs are promising as biomarkers for cancer diagnosis and prognosis and as therapeutic targets or agents to inhibit oncogenic microRNAs or proteins (Kristensen LS, Jakobsen T, Hager H, Kjems J, Nat Rev Clin Oncol 19:188-206, 2022). In this chapter, the procedures for the quantitation of a circRNA in single pancreatic cancer cells using ddPCR are described.

A new droplet digital PCR assay: improving detection of paucibacillary smear-negative pulmonary tuberculosis

BACKGROUND

Smear-negative pulmonary tuberculosis (PTB) is difficult to diagnose. Current diagnosis and treatment monitoring methods have inherent limitations. Droplet digital PCR (ddPCR) is a new technique with high sensitivity. This study presents a novel ddPCR for rapid and sensitive identification of Mycobacterium tuberculosis (MTB).

METHODS

MTB DNA was detected in respiratory specimens from suspected PTB cases using ddPCR assay, which was directed at two different locations within IS6110. We, for the first time, evaluated the clinical diagnostic ability of this ddPCR for paucibacillary smear-negative PTB.

RESULTS

A total of 605 PTB suspects were recruited, including 263 confirmed PTB patients (84.03% from smear-negative PTB) and 342 non-PTB. The sensitivity and specificity of IS6110 ddPCR were 61.22% (95% confidence interval (CI), 55.00%-67.10%) and 95.03% (95% CI, 92.20%-97.10%) for total PTB, and 57.92% (95% CI, 51.10%-64.50%) and 94.57% (95% CI, 91.20%-96.90%) for smear-negative PTB. ddPCR assay outperformed Xpert MTB/RIF (53.08% vs. 28.46%, p = 0.020) in smear-negative PTB detection. Furthermore, effective anti-tuberculosis treatment was linked to significantly lower IS6110 copies detected by ddPCR.

CONCLUSIONS

Herein, we developed and validated a highly sensitive and robust ddPCR assay for MTB quantification in respiratory specimens, which improve diagnosis and therapeutic effect evaluation of smear-negative PTB.

One-Step Digital Droplet Auto-Catalytic Nucleic Acid Amplification with High-Throughput Fluorescence Imaging and Droplet Tracking Computation

Digital droplet technology has emerged as a powerful new tool for biomarker analysis. Temperature cycling, enzymes, and off-chip processes are, nevertheless, always required. Herein, we constructed a digital droplet auto-catalytic hairpin assembly (ddaCHA) microfluidic system to achieve digital quantification of single-molecule microRNA (miRNA). The designed continuous chip integrates droplet generation, incubation, and fluorescence imaging on the chip, avoiding the requirement for extra droplet re-collection and heating operations. Clearly, the digital readout was obtained by partitioning miRNA into many individual pL-sized small droplets in which the target molecule is either present ("positive") or absent ("negative"). Importantly, the suggested enzyme-free auto-catalytic hairpin assembly (aCHA) in droplets successfully mitigated the effects of the external environment and thermal cycling on droplets, and its reaction rate is significantly superior to that of traditional CHA. We got excellent sensitivity with a linear correlation from 1 pM to 10 nM and a detection limit of 0.34 pM in the fluorescence spectrum section, as well as high selectivity to other miRNAs. Furthermore, the minimum target concentration could be reduced to 10 fM based on the high-throughput tracking computation of fluorescent droplets with a self-developed Python script, and the fluorescence intensity distribution agreed well with the theoretical value, demonstrating that it is feasible to detect miRNA efficiently and accurately, which has great potential applications in clinical diagnostics and biochemical research.

MicroRNA-21 expression in single living cells revealed by fluorescence and SERS dual-response microfluidic droplet platform

Analysis of single-cell microRNA is essential to reveal cell heterogeneity at the genetic level. It raises a high demand for single-cell analytical methods because single-cell microRNA sequences are highly similar and small in size and feature low-level expression. Herein, SERS and fluorescence imaging technology were introduced into a microfluidic droplet platform to realize direct in situ, nondestructive, and highly sensitive detection of a small number of microRNA-21 (miR-21) in a single intact living cell. A multifunctional plasmonic nanoprobe was designed by decorating a gold nanoparticle with fluorescent dye (ROX)-labeled probe DNA and capture DNA strands. The dual-signal switching of fluorescence turn-off and SERS turn-on of ROX in response to miR-21 achieves highly sensitive and reliable detection of miR-21 in a single cell. The turn-on of SERS signal with a zero background guarantees the sensitivity of the detection. The fluorescence-SERS simultaneous response strategy was able to mutually corroborate the test results, improving the reliability of determining low-level expression of miR-21. SERS combined with encapsulation of microdroplets provides a feasible way to conduct in situ, nondestructive determination of miR-21 secreted by single cells, avoiding cell lysis and tedious time-consuming steps of miR-21 isolation. As a result, the miR-21 expressed by various types of single cells was investigated by fluorescence imaging and the cellular heterogeneity in miR-21 expression was evaluated accurately and quantitatively by SERS. This research would provide important reference information for understanding the effects of miRNAs on cancer diseases at the single-cell level.

Modern Methods for Assessment of microRNAs

The review discusses modern methods for the quantitative and semi-quantitative analysis of miRNAs, which are small non-coding RNAs affecting numerous biological processes such as development, differentiation, metabolism, and immune response. miRNAs are considered as promising biomarkers in the diagnosis of various diseases.

Integration of the Ligase Chain Reaction with the CRISPR-Cas12a System for Homogeneous, Ultrasensitive, and Visual Detection of microRNA

The ligase chain reaction (LCR), as a classic nucleic acid amplification technique, is popular in the detection of DNA and RNA due to its simplicity, powerfulness, and high specificity. However, homogeneous and ultrasensitive LCR detection is still quite challenging. Herein, we integrate the LCR with a CRISPR-Cas12a system to greatly promote the application of the LCR in a homogeneous fashion. By employing microRNA as the model target, we design LCR probes with specific protospacer adjacent motif sequences and the guide RNA. Then, the LCR is initiated by target microRNA, and the LCR products specifically bind to the guide RNA to activate the Cas12a system, triggering secondary signal amplification to achieve ultrasensitive detection of microRNA without separation steps. Moreover, by virtue of a cationic conjugated polymer, microRNA can not only be visually detected by naked eyes but also be accurately quantified based on RGB ratio analysis of images with no need of sophisticated instruments. The method can quantify microRNA up to 4 orders of magnitude, and the determination limit is 0.4 aM, which is better than those of other reported studies using CRISPR-Cas12a and can be compared with that of the reverse-transcription polymerase chain reaction. This study demonstrates that the CRISPR-Cas12a system can greatly expand the application of the LCR for the homogeneous, ultrasensitive, and visual detection of microRNA, showing great potential in efficient nucleic acid detection and in vitro diagnosis.

MicroRNA-21 electrochemiluminescence biosensor based on Co-MOF-N-(4-aminobutyl)-N-ethylisoluminol/Ti3C2Tx composite and duplex-specific nuclease-assisted signal amplification

A novel electrochemiluminescence (ECL) biosensor for the determination of microRNA-21 (miRNA-21) was developed, based on a hybrid luminescent Co-MOF-ABEI/Ti₃C₂T_x composite as an ECL luminophore combined with a duplex-specific nuclease (DSN)-assisted signal amplification strategy. The synthesized Co-MOF-ABEI/Ti₃C₂T_x composite carrying N-(4-aminobutyl)-N-ethylisoluminol (ABEI) exhibited strong and stable ECL in the presence of reactive oxygen species (ROS). The ECL biosensor was fabricated by adsorbing Co-MOF-ABEI/Ti₃C₂T_x onto a glassy carbon electrode and covalently coupling the probe DNA onto the surface of the Co-MOF-ABEI/Ti₃C₂T_x-modified electrode. In the presence of the target miRNA-21, the DSN selectively cleaved the complementary DNA section (S1) to miRNA-21, resulting in the release of the transduction section (S2) and the reuse of miRNA-21 in the subsequent amplification cycle. The interaction of the stem-loop structure of the probe DNA with the Co-MOF-ABEI/Ti₃C₂T_x-modified glassy carbon electrode with S2 strands led to the opening of the annular part of the probe DNA. Then, the opened guanine (G)-rich sequences of probe DNA were exposed and folded into a hemin/G-quadruplex DNAzyme in the presence of hemin. The catalysis of H₂O₂ to ROS by the hemin/G-quadruplex DNAzyme significantly enhanced ECL intensity, and this intensity was logarithmically proportional to the concentration of target miRNA-21 between 0.00001 and 10 nM, having a limit of detection of 3.7 fM. The designed ECL biosensor can  detect miRNA-21 extracted from HeLa cells, indicating its promising application in clinical diagnosis and disease prognosis analysis.

Easy-to-Operate Co-flow Step Emulsification Device for Droplet Digital Polymerase Chain Reaction

Digital polymerase chain reaction (PCR) plays important roles in the detection and quantification of nucleic acid targets, while there still remain challenges including high cost, complex operation, and low integration of the instrumental system. Here, in this work, a novel microfluidic chip based on co-flow step emulsification is proposed for droplet digital PCR (ddPCR), which can achieve droplet generation, droplet array self-assembly, PCR amplification, and fluorescence detection on a single device. With the combination of single-layer lithography and punching operation, a step microstructure was constructed and it served as the key element to develop a Laplace pressure gradient at the Rayleigh-Plateau instability interface so as to achieve droplet generation. It is demonstrated that the fabrication of step microstructure is low cost, easy-to-operate, and reliable. In addition, the single droplet volume can be adjusted flexibly due to the co-flow design; thus, the ddPCR chip can get an ultrahigh upper limit of quantification to deal with DNA templates with high concentrations. Furthermore, the volume fraction of the resulting droplets in this ddPCR chip can be up to 72% and it results in closely spaced droplet arrays, makes the best of CCD camera for fluorescence detections, and is beneficial for the minimization of a ddPCR system. The quantitative capability of the ddPCR chip was evaluated by measuring template DNA at concentrations from 20 to 50 000 copies/μL. Owing to the characteristics of low cost, easy operation, excellent quantitative capability, and minimization, the proposed ddPCR chip meets the requirements of DNA molecule quantification and is expected to be applied in the point-of-care testing field.

Fluorescence based miniaturized microfluidic and nanofluidic systems for biomedical applications

Over the last two decades miniaturized microfluidic and nanofluidic systems with fluorescence setup emerged as a powerful technological platform for diverse biomedical applications. Bio-macromolecules such as nucleic acids and proteins are the core cellular components, their single molecule analysis allow us to understand biological processes, disease creation and progression, and development of novel treatment policies. Design and development of foolproof treatment methods requires rigorously analysis of nucleic acids and proteins such as length quantifications, sequence profiling, sequence mapping, analysis of conformational changes, analysis and recognition of epigenetic changes, and their interactions with other biomolecules. Miniaturized microfluidic and nanofluidic systems with fluorescence spectroscopy enable worldwide researchers to perform nucleic acids and proteins extractions and single molecule analysis from the trace amount of biological samples. In the present chapter we mostly highlighted over one decade applications of microfluidic and nanofluidic systems for single cell micro ribonucleic acid (miRNA) isolation and detection, deoxyribonucleic acid (DNA) mapping, DNA barcoding, identification of epigenetic mark on single DNA molecule, DNA-protein interactions study, protein sensing, protein sequencing, protein binding kinetics and many other applications. We also presented the recently reported microfluidic platform for the preparation of reproducible unisize aggregation induced emission (AIE) active nanomaterials and their biological applications.

Experimental MicroRNA Detection Methods

MicroRNAs (miRNAs) are considerably small yet highly important riboregulators involved in nearly all cellular processes. Due to their critical roles in posttranscriptional regulation of gene expression, they have the potential to be used as biomarkers in addition to their use as drug targets. Although computational approaches speed up the initial genomewide identification of putative miRNAs, experimental approaches are essential for further validation and functional analyses of differentially expressed miRNAs. Therefore, sensitive, specific, and cost-effective microRNA detection methods are imperative for both individual and multiplex analysis of miRNA expression in different tissues and during different developmental stages. There are a number of well-established miRNA detection methods that can be exploited depending on the comprehensiveness of the study (individual miRNA versus multiplex analysis), the availability of the sample and the location and intracellular concentration of miRNAs. This review aims to highlight not only traditional but also novel strategies that are widely used in experimental identification and quantification of microRNAs.

Current Simultaneous Discrimination of Mismatched MicroRNAs Using Base-Flipping within the α-Hemolysin Latch

The simultaneous discrimination of let-7 microRNAs (miRNAs) would greatly facilitate the early diagnosis and prognosis monitoring of diseases. In this work, a molecular beacon DNA probe was designed to be able to flip out its mismatched cytosine base within the α-hemolysin (α-HL) latch and generate completely separated blocking currents to identify the single-base difference. As a result, the characteristic blocking current of fully matched MB/let-7a and single-base mismatched MB/let-7f was 84.30 ± 0.92 and 87.05 ± 0.86% (confidence level P 95%), respectively. Let-7 miRNA family let-7a and let-7f were completely simultaneously discriminated, which could be attributed to the following strengths. (1) The statistic distribution of blocking current is extremely concentrated with a small relative standard deviation (RSD) of less than 1% and a narrow distribution range. (2) Complete separation is achieved with a high separation resolution of 1.54. (3) The cytosine base flipping out within the α-HL latch provides a universal labeling-free strategy to simultaneously discriminate the single-base mismatch. Overall, the target let-7f sequences were detected with a linear range from 0.001 to 10 pM in human serum samples containing 200 nM let-7a. Great potential has been demonstrated for precise detection, early diagnosis, and prognosis monitoring of diseases related to single-base difference.

A digitalized isothermal nucleic acid testing platform based on a pump-free open droplet array microfluidic chip

Digital PCR has shown great potential for quantitative nucleic acid testing (NAT), but most existing platforms are dependent on large auxiliary equipment (e.g., vacuum pump, amplification instrument, fluorescence microscope) to achieve target dispersion, amplification, signal capture and result analysis. Such complex, expensive and bulky NAT platforms have limited their applications in resource-limited areas, especially for point-of-care testing (POCT). In this work, we designed a digital isothermal NAT platform based on a pump-free open droplet array microfluidic chip. A pump-free microfluidic chip was developed based on an open microdroplet array in the form of thousands of independent microdroplets for spontaneous sample dispersion, without the need for external power. Combined with a handheld fluorescent signal reader based on a smartphone, this digital NAT platform can accurately quantify as low as 1 copy per μL of λDNA. Therefore, our integrated NAT platform, as a potable, robust and low-cost tool for highly accurate NA quantitative analysis, holds great potential for POCT applications.

Endogenous microRNA triggered enzyme-free DNA logic self-assembly for amplified bioimaging and enhanced gene therapy via in situ generation of siRNAs

BACKGROUND

Small interfering RNA (siRNA) has emerged as a kind of promising therapeutic agents for cancer therapy. However, the off-target effect and degradation are the main challenges for siRNAs delivery. Herein, an enzyme-free DNA amplification strategy initiated by a specific endogenous microRNA has been developed for in situ generation of siRNAs with enhanced gene therapy effect on cervical carcinoma.

METHODS

This strategy contains three DNA hairpins (H1, H2/PS and H3) which can be triggered by microRNA-21 (miR-21) for self-assembly of DNA nanowheels (DNWs). Notably, this system is consistent with the operation of a DNA logic circuitry containing cascaded "AND" gates with feedback mechanism. Accordingly, a versatile biosensing and bioimaging platform is fabricated for sensitive and specific analysis of miR-21 in HeLa cells via fluorescence resonance energy transfer (FRET). Meanwhile, since the vascular endothelial growth factor (VEGF) antisense and sense sequences are encoded in hairpin reactants, the performance of this DNA circuit leads to in situ assembly of VEGF siRNAs in DNWs, which can be specifically recognized and cleaved by Dicer for gene therapy of cervical carcinoma.

RESULTS

The proposed isothermal amplification approach exhibits high sensitivity for miR-21 with a detection limit of 0.25 pM and indicates excellent specificity to discriminate target miR-21 from the single-base mismatched sequence. Furthermore, this strategy achieves accurate and sensitive imaging analysis of the expression and distribution of miR-21 in different living cells. To note, compared to naked siRNAs alone, in situ siRNA generation shows a significantly enhanced gene silencing and anti-tumor effect due to the high reaction efficiency of DNA circuit and improved delivery stability of siRNAs.

CONCLUSIONS

The endogenous miRNA-activated DNA circuit provides an exciting opportunity to construct a general nanoplatform for precise cancer diagnosis and efficient gene therapy, which has an important significance in clinical translation.

Anti-Fouling Magnetic Beads Combined with Signal Amplification Strategies for Ultra-Sensitive and Selective Electrochemiluminescence Detection of MicroRNAs in Complex Biological Media

Herein, an electrochemiluminescence (ECL) microRNA biosensor based on anti-fouling magnetic beads (MBs) and two signal amplification strategies was developed. The newly designed anti-fouling dendritic peptide was wrapped on the surfaces of MBs to make them resistant to nonspecific adsorption of biomolecules in complex biological samples so as to realize accurate and selective target recognition. One of the amplification strategies was achieved through nucleic acid cycle amplification based on the DNAzyme on the surfaces of MBs. Then, the output DNA generated by the nucleic acid cycle amplification program stimulated the hybrid chain reaction (HCR) process on the modified electrode surface to generate the other amplification of the ECL response. Titanium dioxide nanoneedles (TiO₂ NNs), as a co-reaction accelerator of the Ru(bpy)₂(cpaphen)²⁺ and tripropylamine (TPrA) system, were wrapped with the electrodeposited polyaniline (PANI) on the electrode surface to enhance the ECL intensity of Ru(bpy)₂(cpaphen)²⁺. The conducting polymer PANI can not only immobilize the TiO₂ NNs but also improve the conductivity of the modified electrodes. The biosensor exhibited ultra-high sensitivity and excellent selectivity toward the detection of miRNA 21, with a detection limit of 0.13 fM. More importantly, with the anti-fouling MBs as a unique separation tool, this ECL biosensor was capable of assaying targets in complex biological media such as serum and cell lysate.

Highly convenient and highly specific-and-sensitive PCR using Se-atom modified dNTPs

Primer design and condition optimization for PCR are tedious and labour-intensive. To conveniently achieve high selectivity, sensitivity and robustness, herein, we first report a new strategy with Se-dNTPs to enhance PCR specificity (over 240-fold) and sensitivity (up to single-digit), effectively eliminating non-specific products and simplifing PCR design and optimization.

Ultrasensitive homogeneous detection of microRNAs in a single cell with specifically designed exponential amplification

We firstly developed an ultrasensitive method based on specifically designed exponential amplification for miRNA detection with simple operation in homogeneous solutions. The proposed assay can detect miRNAs at a concentration as low as 1 aM and can be successfully applied for routine miRNA detection in a single cell.

Ultra-specific genotyping of single nucleotide variants by ligase-based loop-mediated isothermal amplification coupled with a modified ligation probe

Specific and accurate detection of single nucleotide variants (SNVs) plays significant roles in pathogenic gene research and clinical applications. However, the sensitive but ultra-specific detection of rare variants in biological samples still remains challenging. Herein, we report a novel, robust and practical SNV assay by integrating the outstanding features of high selectivity of an artificial mismatched probe, and the powerful loop-mediated isothermal amplification. In this strategy, we rationally introduce artificial mismatched bases into the 3′-terminal regions of the probe located in the ligation region to reduce the risk of nonspecific ligation, which can dramatically improve the specificity for the SNV assay. The proposed method can discern as little as 0.01% mutant DNA in the high background of wild-type DNA with high sensitivity (10 aM). In virtue of its outstanding performance, the artificial mismatched probe may also be employed and expanded in various DNA and RNA genetic analyses with ligase-assisted approaches, showing great potential in biomedical research, clinical diagnostics, and bioanalysis.

An artificial mismatched base introduced in a ligation probe can effectively reduce nonspecific ligation and improve the specificity for SNV assay.

Highly Sensitive and Specific Mass Spectrometric Platform for miRNA Detection Based on the Multiple-Metal-Nanoparticle Tagging Strategy

The multiple-metal-nanoparticle tagging strategy has generally been applied to the multiplexed detection of multiple analytes of interest such as microRNAs (miRNAs). Herein, it was used for the first time to improve both the specificity and sensitivity of a novel mass spectroscopic platform for miRNA detection. The mass spectroscopic platform was developed through the integration of the ligation reaction, hybridization chain reaction amplification, multiple-metal-nanoparticle tagging, and inductively coupled plasma mass spectrometry. The high specificity resulted from the adoption of the ligation reaction is further enhanced by the multiple-metal-nanoparticle tagging strategy. The combination of hybridization chain reaction amplification and metal nanoparticle tagging endows the proposed platform with the feature of high sensitivity. The proposed mass spectrometric platform achieved quite satisfactory quantitative results for Let-7a in real-world cell line samples with accuracy comparable to that of the real-time quantitative reverse-transcriptase polymerase chain reaction method. Its limit of detection and limit of quantification for Let-7a were experimentally determined to be about 0.5 and 10 fM, respectively. Furthermore, due to the unique way of utilizing the multiple-metal-nanoparticle tagging strategy, the proposed platform can unambiguously discriminate between the target miRNA and nontarget ones with single-nucleotide polymorphisms based on their response patterns defined by the relative mass spectral intensities among the multiple tagged metal elements and can also provide location information of the mismatched bases. Its unique advantages over conventional miRNA detection methods make the proposed platform a promising and alternative tool in the fields of clinical diagnosis and biomedical research.

Nucleic Acids Analysis

Nucleic acids are natural biopolymers of nucleotides that store, encode, transmit and express genetic information, which play central roles in diverse cellular events and diseases in living things. The analysis of nucleic acids and nucleic acids-based analysis have been widely applied in biological studies, clinical diagnosis, environmental analysis, food safety and forensic analysis. During the past decades, the field of nucleic acids analysis has been rapidly advancing with many technological breakthroughs. In this review, we focus on the methods developed for analyzing nucleic acids, nucleic acids-based analysis, device for nucleic acids analysis, and applications of nucleic acids analysis. The representative strategies for the development of new nucleic acids analysis in this field are summarized, and key advantages and possible limitations are discussed. Finally, a brief perspective on existing challenges and further research development is provided.

PCR past, present and future

PCR has become one of the most valuable techniques currently used in bioscience, diagnostics and forensic science. Here we review the history of PCR development and the technologies that have evolved from the original PCR method. Currently, there are two main areas of PCR utilization in bioscience: high-throughput PCR systems and microfluidics-based PCR devices for point-of-care (POC) applications. We also discuss the commercialization of these techniques and conclude with a look into their modifications and use in innovative areas of biomedicine. For example, real-time reverse transcription PCR is the gold standard for SARS-CoV-2 diagnoses. It could also be used for POC applications, being a key component of the sample-to-answer system.

Isothermal digital detection of microRNAs using background-free molecular circuit

MicroRNAs, a class of transcripts involved in the regulation of gene expression, are emerging as promising disease-specific biomarkers accessible from tissues or bodily fluids. However, their accurate quantification from biological samples remains challenging. We report a sensitive and quantitative microRNA detection method using an isothermal amplification chemistry adapted to a droplet digital readout. Building on molecular programming concepts, we design a DNA circuit that converts, thresholds, amplifies, and reports the presence of a specific microRNA, down to the femtomolar concentration. Using a leak absorption mechanism, we were able to suppress nonspecific amplification, classically encountered in other exponential amplification reactions. As a result, we demonstrate that this isothermal amplification scheme is adapted to digital counting of microRNAs: By partitioning the reaction mixture into water-in-oil droplets, resulting in single microRNA encapsulation and amplification, the method provides absolute target quantification. The modularity of our approach enables to repurpose the assay for various microRNA sequences.

An emulsion-free digital flow cytometric platform for the precise quantification of microRNA based on single molecule extension-illuminated microbeads (dFlowSeim)

An emulsion-free digital flow cytometric platform is developed for precise quantification of nucleic acids based on single molecule extension-illuminated microbeads.