Highly sensitive and simultaneous detection of microRNAs in serum using stir-bar assisted magnetic DNA nanospheres-encoded probes

CRISPR/Cas12a-coupled multiplexed strand displacement amplification for miRNA155 one-tube detection: via a dual-cavity PCR tube

A CRISPR/Cas12a-coupled multiplexed strand displacement amplification (CMSDA) for the detection of miR155 has been developed. Non-specific amplification was avoided by designing a single-stranded DNA template with a hairpin structure. The detection target miR155 was used as a primer to initiate a multiple-strand displacement reaction to produce abundant ssDNA. ssDNA was recognized by the Cas12a/CrRNA binary complex, activating the trans-cleaving activity of Cas12a. The multiple-strand displacement reaction is more efficiently detected compared with a single-strand displacement reaction. The detection range is from 250 pM to 1 nM, and the limit of the detection is 6.5 pM. The proposed method showed a good applicability in complex serum environments, indicating that the method has a broad prospect for disease detection and clinical application. In addition, we designed a dual-cavity PCR tube, which realized one-tube detection of miRNA155 and avoided open-cap contamination.

Nanomaterials in electrochemical nanobiosensors of miRNAs

Nanomaterial-based biosensors have received significant attention owing to their unique properties, especially enhanced sensitivity. Recent advancements in biomedical diagnosis have highlighted the role of microRNAs (miRNAs) as sensitive prognostic and diagnostic biomarkers for various diseases. Current diagnostics methods, however, need further improvements with regards to their sensitivity, mainly due to the low concentration levels of miRNAs in the body. The low limit of detection of nanomaterial-based biosensors has turned them into powerful tools for detecting and quantifying these biomarkers. Herein, we assemble an overview of recent developments in the application of different nanomaterials and nanostructures as miRNA electrochemical biosensing platforms, along with their pros and cons. The techniques are categorized based on the nanomaterial used.

Electrochemical Biosensors for Whole Blood Analysis: Recent Progress, Challenges, and Future Perspectives

Whole blood, as one of the most significant biological fluids, provides critical information for health management and disease monitoring. Over the past 10 years, advances in nanotechnology, microfluidics, and biomarker research have spurred the development of powerful miniaturized diagnostic systems for whole blood testing toward the goal of disease monitoring and treatment. Among the techniques employed for whole-blood diagnostics, electrochemical biosensors, as known to be rapid, sensitive, capable of miniaturization, reagentless and washing free, become a class of emerging technology to achieve the target detection specifically and directly in complex media, e.g., whole blood or even in the living body. Here we are aiming to provide a comprehensive review to summarize advances over the past decade in the development of electrochemical sensors for whole blood analysis. Further, we address the remaining challenges and opportunities to integrate electrochemical sensing platforms.

A novel detection of MicroRNA based on homogeneous electrochemical sensor with enzyme-assisted signal amplification

Rapid and sensitive detection of microRNAs is of great importance in biological researches and cancer diagnosis. Herein, we proposed a novel homogeneous electrochemical sensor to detect microRNA-21 (miRNA-21) using functionalized magnetic nanoparticles combined with enzyme-assisted signal amplification. The biotinylated capture probe (CP) labeled magnetic nanoparticles can capture miRNA-21 and introduce streptavidin-conjugated hydroxyapatite (HAP) nanoparticles. In the presence of miRNA-21, hybridization between RNA and DNA results in the formation of RNA/DNA duplexes, and then duplex-specific nuclease (DSN) cleave the duplexes to digest the capture chain and release the miRNA-21 in a loop. Meanwhile, the HAP nanoparticles strip from the magnetic nanoparticles and electrochemical signal by the reaction of HAP with molybdate is changed. The current variation before and after incubation with miRNA-21 is linearly correlated with the miRNA-21 concentration between 1 aM and 1 pM with a low detection limit (LOD) of 0.27 aM. Remarkably, the expression of miRNA-21 in human serum and different cell lysate was successfully performed, which fully demonstrates the great practical potentials in biomedical diagnostics and clinical therapeutics.

Nucleotide detection mechanism and comparison based on low-dimensional materials: A review

The recent pandemic has led to the fabrication of new nucleic acid sensors that can detect infinitesimal limits immediately and effectively. Therefore, various techniques have been demonstrated using low-dimensional materials that exhibit ultrahigh detection and accuracy. Numerous detection approaches have been reported, and new methods for impulse sensing are being explored. All ongoing research converges at one unique point, that is, an impetus: the enhanced limit of detection of sensors. There are several reviews on the detection of viruses and other proteins related to disease control point of care; however, to the best of our knowledge, none summarizes the various nucleotide sensors and describes their limits of detection and mechanisms. To understand the far-reaching impact of this discipline, we briefly discussed conventional and nanomaterial-based sensors, and then proposed the feature prospects of these devices. Two types of sensing mechanisms were further divided into their sub-branches: polymerase chain reaction and photospectrometric-based sensors. The nanomaterial-based sensor was further subdivided into optical and electrical sensors. The optical sensors included fluorescence (FL), surface plasmon resonance (SPR), colorimetric, and surface-enhanced Raman scattering (SERS), while electrical sensors included electrochemical luminescence (ECL), microfluidic chip, and field-effect transistor (FET). A synopsis of sensing materials, mechanisms, detection limits, and ranges has been provided. The sensing mechanism and materials used were discussed for each category in terms of length, collectively forming a fusing platform to highlight the ultrahigh detection technique of nucleotide sensors. We discussed potential trends in improving the fabrication of nucleotide nanosensors based on low-dimensional materials. In this area, particular aspects, including sensitivity, detection mechanism, stability, and challenges, were addressed. The optimization of the sensing performance and selection of the best sensor were concluded. Recent trends in the atomic-scale simulation of the development of Deoxyribonucleic acid (DNA) sensors using 2D materials were highlighted. A critical overview of the challenges and opportunities of deoxyribonucleic acid sensors was explored, and progress made in deoxyribonucleic acid detection over the past decade with a family of deoxyribonucleic acid sensors was described. Areas in which further research is needed were included in the future scope.

Formation of miRNA Nanoprobes-Conjugation Approaches Leading to the Functionalization

Recently, microRNAs (miRNA) captured the interest as novel diagnostic and prognostic biomarkers, with their potential for early indication of numerous pathologies. Since miRNA is a short, non-coding RNA sequence, the sensitivity and selectivity of their detection remain a cornerstone of scientific research. As such, methods based on nanomaterials have emerged in hopes of developing fast and facile approaches. At the core of the detection method based on nanotechnology lie nanoprobes and other functionalized nanomaterials. Since miRNA sensing and detection are generally rooted in the capture of target miRNA with the complementary sequence of oligonucleotides, the sequence needs to be attached to the nanomaterial with a specific conjugation strategy. As each nanomaterial has its unique properties, and each conjugation approach presents its drawbacks and advantages, this review offers a condensed overview of the conjugation approaches in nanomaterial-based miRNA sensing. Starting with a brief recapitulation of specific properties and characteristics of nanomaterials that can be used as a substrate, the focus is then centered on covalent and non-covalent bonding chemistry, leading to the functionalization of the nanomaterials, which are the most commonly used in miRNA sensing methods.

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.

An AC electrokinetics-based electrochemical aptasensor for the rapid detection of microRNA-155

Traditional immunosensors are often limited by low sensitivity and long detection times, for they usually depend on passive diffusion-dominated transport of target analytes for the binding reaction with a bio-recognition element such as enzymes, antibodies, and aptamers. Numerous studies rely on electric field manipulation by using alternating current (AC) electrokinetics to enhance the hybridization rate and reduce the hybridization time for faster and more efficient detection. This study demonstrated a rapid electrochemical aptasensor integrated with an AC electroosmotic (ACEO) flow phenomenon for the enhanced target hybridization of microRNA-155 (miR-155). Optimization of the electrokinetic conditions for target collection resulted in a saturation point after 75 s miR-155 was detected within the range of 1 aM-10 pM with a detection limit of 1 aM, which is 100 times lower and about 50 times faster compared with the conventional diffusion-dependent detection done for 1 h. The detection was also done in spiked serum samples, and a concentration range within the required detection range was obtained. The highly sensitive and specific results allow for the rapid and real-time sensing of target biomarkers, which can be used for the early detection of infection.

Carbon nanodot-based electrogenerated chemiluminescence biosensor for miRNA-21 detection

A simple carbon nanodot–based electrogenerated chemiluminescence biosensor is described for sensitive and selective detection of microRNA-21 (miRNA-21), a biomarker of several pathologies including cardiovascular diseases (CVDs). The photoluminescent carbon nanodots (CNDs) were obtained using a new synthesis method, simply by treating tiger nut milk in a microwave reactor. The synthesis is environmentally friendly, simple, and efficient. The optical properties and morphological characteristics of the CNDs were exhaustively investigated, confirming that they have oxygen and nitrogen functional groups on their surfaces and exhibit excitation-dependent fluorescence emission, as well as photostability. They act as co-reactant agents in the anodic electrochemiluminescence (ECL) of [Ru(bpy)₃]²⁺, producing different signals for the probe (single-stranded DNA) and the hybridized target (double-stranded DNA). These results paved the way for the development of a sensitive ECL biosensor for the detection of miRNA-21. This was developed by immobilization of a thiolated oligonucleotide, fully complementary to the miRNA-21 sequence, on the disposable gold electrode. The target miRNA-21 was hybridized with the probe on the electrode surface, and the hybridization was detected by the enhancement of the [Ru(bpy)₃]²⁺/DNA ECL signal using CNDs. The biosensor shows a linear response to miRNA-21 concentration up to 100.0 pM with a detection limit of 0.721 fM. The method does not require complex labeling steps, and has a rapid response. It was successfully used to detect miRNA-21 directly in serum samples from heart failure patients without previous RNA extraction neither amplification process.

Multicolor fluorescence encoding of different microRNAs in lung cancer tissues at the single-molecule level

The simultaneous detection of multiple microRNAs (miRNAs) will facilitate early clinical diagnosis. Herein, we demonstrate the integration of multicolor fluorophore-encoded cascade signal amplification with single-molecule detection for simultaneous measurement of different miRNAs in lung cancer tissues. This assay involves two linear templates and two circular templates without the requirement of any fluorescent-labeled probes. The binding of target miRNAs to their corresponding linear templates initiates the cyclic strand displacement amplification, generating many triggers which can specifically hybridize with the corresponding biotin-labeled AP probes to initiate the apurinic/apyrimidic endonuclease 1-assisted cyclic cleavage reaction for the production of more biotin-labeled primers for each miRNA. The resultant two primers can react with their corresponding circular templates to initiate rolling circle amplification which enables the incorporation of Cy5-dCTP/Cy3-dGTP nucleotides, resulting in the simultaneous production of abundant biotin-/multiple Cy5/Cy3-labeled DNA products. After magnetic separation and exonuclease cleavage, the amplified products release abundant Cy5 and Cy3 fluorescent molecules which can be simply monitored by single-molecule detection, with Cy3 indicating miR-21 and Cy5 indicating miR-155. This assay involves three consecutive amplification reactions, enabling the conversion of extremely low abundant target miRNAs into large numbers of Cy5/Cy3 fluorophore-encoded DNA products which can release abundant fluorescent molecules for the generation of amplified signals. This assay exhibits high sensitivity, good selectivity, and the capability of multiplexed assay. This method can simultaneously quantify miR-155 and miR-21 in living cells and in lung cancer tissues, and it can distinguish the expression of miRNAs between non-small cell lung cancer patients and healthy persons. The accuracy and reliability of the proposed method are further validated by quantitative reverse transcription polymerase chain reaction.

Highly Sensitive Detection of miRNA-155 Using Molecular Beacon-Functionalized Monolayer MoS₂ Nanosheet Probes with Duplex-Specific Nuclease-Mediated Signal Amplification

MicroRNA-155 (miRNA-155) as a characteristic myeloma-associated biomarker exhibits significant potential application in the diagnosis of multiple myeloma (MM). In this paper, a novel type of molecular beacon (MB)-functionalized monolayer MoS₂ nanosheet probe was proposed as fluorescent probe for high-sensitive assays of miRNA-155that uses a duplexspecificnuclease (DSN) enzyme to amplify the fluorescence signal. The preparation and detection conditions of the fluorescent probes were optimized in some aspects, such as the concentration of MoS₂ (0.80 μM) and DSN (0.2 U), and the incubation time of DSN (30 min). The probesexhibited a sensitive fluorescence response to miRNA-155 and the fluorescence signal of the assay was significantly amplified by the cleavage of DSN. The relationship between F/F₀ and logC miRNA follows a linear calibration curve, and the limit of detection (LOD) of miRNA-155 in 10% human serum is calculated to be 10.96 fM based on this relationship. The good performance and fluorescence amplification effect of the fluorescent probe were confirmed by studying the recovery of miRNA-155 in 10% human serum, which was ranged from 98.32% to 106.3% with a relative standard deviation of less than 4.14%. Besides, the high expression of miRNA-155 in clinic blood of MM patients was sensitively distinguished from healthy peoples by using the proposed probes. The proposed novel fluorescent probe based on the DSN can be used to detect miRNA-155 in human serum and provide a potential, convenient and reliable tool for diagnosis of MM.

Novel electrochemical biosensor based on Exo III-assisted digestion of dsDNA polymer from hybridization chain reaction in homogeneous solution for CYFRA 21-1 DNA assay

A novel electrochemical biosensing strategy was proposed to detect cytokeratin fragment antigen 21-1 (CYFRA 21-1) DNA based on Exo III-assisted digestion of dsDNA polymer (EADDP) from hybridization chain reaction (HCR). Primarily, the presence of target can drive a catalytic hairpin assembly (CHA) reaction, which was aimed to achieve target recognition and circulation. Then the HCR can be triggered for further signal amplification and generate long dsDNA polymer with signal tags. Subsequently, the introduction of Exo III can digest the long dsDNA polymer to produce large amounts of double signal fragments (DSFs). The above experiments were all carried out in homogeneous solution. Finally, the released DSF can be captured onto the electrode directly by capture probe (CP) and a highly amplified electrochemical signal can be detected. The EADDP in homogeneous solution circumvented complex solid-liquid interface reaction and tedious operation steps on electrode. Besides, one target can be converted into abundant DSFs, which greatly improved the sensitivity. This biosensor exhibited a low detection limit (0.0348 fM) and wide linear range (5 fM ∼ 50 nM) for CYFRA 21-1 DNA biosensing with reliable specificity and stability.

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-probe fluorescent biosensor based on T7 exonuclease-assisted target recycling amplification for simultaneous sensitive detection of microRNA-21 and microRNA-155

Effective and simultaneous monitoring of the abnormal expression of certain microRNAs (miRNAs), especially for miRNA-21 and miRNA-155, can indicate drug resistance in lung cancer. In this work, T7 exonuclease (T7 Exo)-assisted target recycling amplification coupled with the extensive fluorescence quenching of graphene oxide (GO) was designed for the simultaneous detection of miRNA-21 and miRNA-155 using FAM- and ROX-labeled single-strand DNA probes. Through this method, the variable emission intensities of FAM and ROX caused by the introduction of miRNA-21 and miRNA-155, respectively, were obtained with high sensitivity. The method exhibited excellent analytical performance for simultaneous detection of miRNA-21 and miRNA-155 without cross-interference. The linear range was from 0.005 nM to 5 nM over three orders of magnitude, with detection limits as low as 3.2 pM and 4.5 pM for miRNA-21 and miRNA-155, respectively. Furthermore, the recovery (92.49-103.67%) and relative standard deviation (RSD < 4.8%) of the standard addition test of miRNA-21 and miRNA-155 in human plasma suggested the potential for drug resistance warning in clinical practice via this simple strategy. A homogeneous T7 Exo-assisted signal amplification combined with GO quenching platform was developed for accurate, sensitive and simultaneous analysis of miRNA-21 and miRNA-155 for drug resistance warning in lung cancer. This simple method exhibited a wide linear range and low LODs for miR-21 and miR-155.

Electrochemical Biosensors for Detection of MicroRNA as a Cancer Biomarker: Pros and Cons

Cancer is the second most fatal disease in the world and an early diagnosis is important for a successful treatment. Thus, it is necessary to develop fast, sensitive, simple, and inexpensive analytical tools for cancer biomarker detection. MicroRNA (miRNA) is an RNA cancer biomarker where the expression level in body fluid is strongly correlated to cancer. Various biosensors involving the detection of miRNA for cancer diagnosis were developed. The present review offers a comprehensive overview of the recent developments in electrochemical biosensor for miRNA cancer marker detection from 2015 to 2020. The review focuses on the approaches to direct miRNA detection based on the electrochemical signal. It includes a RedOx-labeled probe with different designs, RedOx DNA-intercalating agents, various kinds of RedOx catalysts used to produce a signal response, and finally a free RedOx indicator. Furthermore, the advantages and drawbacks of these approaches are highlighted.

Magnetic nanoparticle-based amplification of microRNA detection in body fluids for early disease diagnosis

Circulating biomarkers such as microRNAs (miRNAs), short noncoding RNA strands, represent prognostic and diagnostic indicators for a variety of physiological disorders making their detection and quantification an attractive approach for minimally invasive early disease diagnosis. However, highly sensitive and selective detection methods are required given the generally low abundance of miRNAs in body fluids together with the presence of large amounts of other potentially interfering biomolecules. Although a variety of miRNA isolation and detection methods have been established in clinics, they usually require trained personnel and often constitute labor-, time- and cost-intensive approaches. During the last years, nanoparticle-based biosensors have received increasing attention due to their superior detection efficiency even in very low concentration regimes. This is based on their unique physicochemical properties in combination with their high surface area that allows for the immobilization of multiple recognition sites resulting in fast and effective recognition of analytes. Among various materials, magnetic nanoparticles have been identified as useful tools for the separation, concentration, and detection of miRNAs. Here, we review state-of-the-art technology with regard to magnetic particle-based miRNA detection from body fluids, critically discussing challenges and future perspective of such biosensors while comparing their handling, sensitivity as well as selectivity against the established miRNA isolation and detection methods.