Enzyme-free and multiplexed microRNA detection using microRNA-initiated DNA molecular motor

In this work, we have developed a sensitive, simple, and enzyme-free assay for detection of microRNAs (miRNAs) by means of a DNA molecular motor consisting of two stem-loop DNAs with identical stems and complementary loop domains. In the presence of miRNA target, it can hybridize with one of the stem-loop DNA to open the stem and to produce a miRNA/DNA hybrid and a single strand (ss) DNA, the ssDNA will in turn hybridize with another stem-loop DNA and finally form a double strand (ds) DNA to release the miRNA. One of the stem-loop DNA is double-labeled by a fluorophore/quencher pair with efficiently quenched fluorescence. The formation of dsDNA can produced specific fluorescence signal for miRNA detection. The released miRNA will continuously initiate the next hybridization of the two stem-loop DNAs to form a cycle-running DNA molecular motor, which results in great fluorescence amplification. With the efficient signal amplification, as low as 1 pmol/L miRNA target can be detected and a wide dynamic range from 1 pmol/L to 2 nmol/L is also obtained. Moreover, by designing different stem-loop DNAs specific to different miRNA targets and labeling them with different fluorophores, multiplexed miRNAs can be simultaneously detected in one-tube reaction with the synchronous fluorescence spectrum (SFS) technique.     

A pico-HPLC-LIF system for the amplification-free determination of multiple miRNAs in cells

MicroRNAs are a class of important biomarkers,and the simultaneous detection of multiple miRNAs can provide valuable information about many diseases and biological processes.Amplification-free determination has been developed for the analysis of multiple miRNAs because of its characteristic low cost and high fidelity.Herein,a method for the amplification-free analysis and simultaneous detection of multiple miRNAs based on a so-called pico-HPLC-LIF system is described.In this process,a bare open capilla ry with an inner diameter of 680 nm is used as a sepa ration column for a sample volume of several hundreds of femtoliters(300 fL),followed by separation and detection.The technique has a zeptomolar limit of detection.The method was applied to detect cellular miRNA from adenocarcinomic human alveolar basal epithelial(A549) cell extracts,and the simultaneous detection of the mir-182,miR-155,and let-7 a was achieved.The results showed that the expression of mir-182 and miR-155 was up-regulated and that of let-7 a was down-regulated in A549 cells.This method for multiple miRNAs detection is expected to have broad applications in miRNA-based disease diagnosis,prognosis,treatment,and monitoring.     

Simultaneous and ultrasensitive detection of multiple microRNAs by single-molecule fluorescence imaging

Cell status changes are typically accompanied by the simultaneous changes of multiple microRNA (miRNA) levels. Thus, simultaneous and ultrasensitive detection of multiple miRNA biomarkers shows great promise in early cancer diagnosis. Herein, a facile single-molecule fluorescence imaging assay was proposed for the simultaneous and ultrasensitive detection of multiple miRNAs using only one capture anti-DNA/RNA antibody (S9.6 antibody). Two complementary DNAs (cDNAs) designed to hybridize with miRNA-21 and miRNA-122 were labelled with Cy3 (cDNA1) and Cy5 (cDNA2) dyes at their 5′-ends, respectively. After hybridization, both miRNA-21/cDNA1 and miRNA-122/cDNA2 complexes were captured by S9.6 antibodies pre-modified on a coverslip surface. Subsequently, the Cy3 and Cy5 dyes on the coverslip surface were imaged by the single-molecule fluorescence setup. The amount of miRNA-21 and miRNA-122 was quantified by counting the image spots from the Cy3 and Cy5 dye molecules in the green and red channels, respectively. The proposed assay displayed high specificity and sensitivity for singlet miRNA detection both with a detection limit of 5 fM and for multiple miRNA detection both with a detection limit of 20 fM. Moreover, it was also demonstrated that the assay could be used to detect multiple miRNAs simultaneously in human hepatocellular cancer cells (HepG2 cells). The proposed assay provides a novel biosensing platform for the ultrasensitive and simple detection of multiple miRNA expressions and shows great prospects for early cancer diagnosis.

A single-molecule assay for multiple microRNA detection.     

A Rapid,Amplification‐Free,and Sensitive Diagnostic Assay for Single‐Step Multiplexed Fluorescence Detection of MicroRNA

The importance of microRNA (miRNA) dysregulation for the development and progression of diseases and the discovery of stable miRNAs in peripheral blood have made these short‐sequence nucleic acids next‐generation biomarkers. Here we present a fully homogeneous multiplexed miRNA FRET assay that combines careful biophotonic design with various RNA hybridization and ligation steps. The single‐step, single‐temperature, and amplification‐free assay provides a unique combination of performance parameters compared to state‐of‐the‐art miRNA detection technologies. Precise multiplexed quantification of miRNA‐20a, ‐20b, and ‐21 at concentrations between 0.05 and 0.5 nM in a single 150 μL sample and detection limits between 0.2 and 0.9 nM in 7.5 μL serum samples demonstrate the feasibility of both high‐throughput and point‐of‐care clinical diagnostics.     

Streptavidin-enhanced surface plasmon resonance biosensor for highly sensitive and specific detection of microRNA

We are presenting a method for sensitive and specific detection of microRNA (miRNA) using surface plasmon resonance. A thiolated capture DNA probe with a short complete complementary sequence was immobilized on the gold surface of the sensor to recognize the part sequence of target miRNA, and then an oligonucleotide probe linked to streptavidin was employed to bind the another section of the target. The use of the streptavidin-oligonucleotide complex caused a ~5-fold increase in signal, improved the detection sensitivity by a factor of ~24, and lowered the detection limit to 1.7 fmol of miR-122. This specificity allowed a single mismatch in the target miRNA to be discriminated. The whole assay takes 30 min, and the surface of the sensor can be regenerated at least 30 times without loss in performance. The method was successfully applied to the determination of miRNA spiked into human total RNA samples.

An Aptamer-Based Competitive Fluorescence Quenching Assay for IgE

A simple competitive fluorescence quenching assay based on aptamer was developed for IgE detection. Two DNA probes were used. One is 5′-end fluorescein-labeled IgE aptamer; the other is 3′-end DABCYL-labeled short DNA, which would hybridize with IgE aptamer to quench the fluorescence. In the presence of IgE, the aptamer-IgE complex formed is strong enough to prevent the short DNA probes hybridizing with the bounded aptamer probes, which results in the less decrease of fluorescence intensity. The signal change was found to be proportional to the concentration of IgE from 0.35 to 35 nM with a detection limit of 0.17 nM.     

Gold nanoparticle enhanced surface plasmon resonance imaging of microRNA-155 using a functional nucleic acid-based amplification machine

MicroRNAs (miRNAs) are considered as being promising biomarkers for hematological malignancies, their aging, progression and prognosis. The authors have developed a method for the detection of miRNA-155 by using surface plasmon resonance (SPR) imaging coupled to a nucleic acid-based amplification strategy using gold nanoparticles (AuNPs). The target miRNA-155 is captured by surface-bound DNA probes. After hybridization, DNA-AuNP are employed for signal amplification via DNA sandwich assembly, resulting in a large increase in the SPR signal. This method can detect miRNA-155 in concentrations down to 45 pM and over dynamic that extends from 50 pM to 5 nM. The assay is highly specific and can discriminate even a single base mismatch. It also is reproducible, precise, and was successfully applied to the determination of miRNA-155 in spiked real samples where it gave recoveries in the range between 86% and 98%. This biosensor provides an alternative approach for miRNA detection in biomedical research and clinical diagnosis, which is highly effective and efficient.

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Graphical abstract Schematic of a surface plasmon resonance imaging biosensor for detection of miRNA-155 using strand displacement amplification and gold nanoparticle.

     

Fluorescence based turn-on strategy for determination of microRNA-155 using DNA-templated copper nanoclusters

The authors report on a new approach for the determination of the breast cancer biomarker microRNA-155 (miRNA-155). It is based on the measurement of the fluorescence shift of oligonucleotide-templated copper nanoclusters (DNA-CuNC). A probe DNA was designed that acts as a template for the preparation of CuNC which, under 400 nm excitation, exhibit strong fluorescence enhancement at 490 nm and a 90 nm Stokes shift after binding to target miRNA-155 and formation of a DNA-RNA heteroduplex. Under the optimal conditions, the fluorescence of the DNA-CuNC increases with increasing concentration of miRNA-155 in the range from 50 pM to 10 nM, with a 11 pM detection limit. The assay has excellent selectivity over noncomplementary RNA. The method was applied to the determination of miRNA-155 in the presence of human plasma and saliva.

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Graphical abstract Schematic of the detection strategy that relies on the fluorescence shift of DNA-CuNCs resulting from the specific binding of DNA-CuNCs with target miRNA-155. Fluorescence intensities are linearly proportional to the concentrations of target RNA from 50 pM to 10 nM.

     

Sensitive and selective DNA probe based on “turn-on” photoluminescence of C-dots@RGO

In this study, highly hydrophilic and photoluminescent sheets of reduced graphene oxide decorated with carbon dots (C-dots@RGO), methylene blue (MB), and a probe DNA have been used for the detection of DNA. The photoluminescence of C-dots@RGO is quenched by MB, which is restored in the presence of a target DNA. The combination of the C-dots@RGO, MB, and a DNA probe is selective for perfectly matched DNA over mismatched DNA, mainly because relative to single-stranded DNA, double-stranded DNA intercalates more strongly with MB, but interacts more weakly with RGO. In the presence of a target DNA, MB intercalates with the as-formed double-stranded DNA and is released from the surface of C-dots@RGO, leading to “turn-on” photoluminescence. The practicality of this assay has been validated by the determination of tumor suppressor gene BRCA1, with linearity over the concentration range from 25 to 250 nM and a limit of detection (LOD, at a signal-to-noise ratio of 3) of 14.6 nM. The C-dots@RGO probe provides higher specificity towards target DNA than towards common salts, carbohydrates, amino acids, and proteins found in real samples. Having the advantages of simplicity, cost-effectiveness, selectivity, and sensitivity, the DNA-P/C-dots@RGO–MB probe on microwells has been successfully employed for the detection of DNA, suggesting its potential for multiple analyses of DNA targets when various DNA probes are employed.     

Simultaneous and multiplex detection of exosomal microRNAs based on the asymmetric Au@Au@Ag probes with enhanced Raman signal

Simultaneous and quantitative detection of multiple exosomal micro RNAs(miRNAs) was successfully performed by a surface-enhanced Raman scattering(SERS) assay consisting of Raman probes and capture probes. In this design, the asymmetric core-shell structured Au@Au@Ag nanoparticles were first synthesized by layer-by-layer self-assembly method and modified with different Raman molecules and recognition sequences(poly A-DNA) to prepare the surface-enhanced Raman probes. Then, the streptavidinmodifie...     

Ratiometric Detection of microRNA Using Hybridization Chain Reaction and Fluorogenic Silver Nanoclusters

miRNA (miR)-155 is a potential biomarker for breast cancers. We aimed at developing a nanosensor for miR-155 detection by integrating hybridization chain reaction (HCR) and silver nanoclusters (AgNCs). HCR serves as an enzyme-free and isothermal amplification method, whereas AgNCs provide a built-in fluorogenic detection probe that could simplify the downstream analysis. The two components were integrated by adding a nucleation sequence of AgNCs to the hairpin of HCR. The working principle was based on the influence of microenvironment towards the hosted AgNCs, whereby unfolding of hairpin upon HCR has manipulated the distance between the hosted AgNCs and cytosine-rich toehold region of hairpin. As such, the dominant emission of AgNCs changed from red to yellow in the absence and presence of miR-155, enabling a ratiometric measurement of miR with high sensitivity. The limit of detection (LOD) of our HCR-AgNCs nanosensor is 1.13 fM in buffered solution. We have also tested the assay in diluted serum samples, with comparable LOD of 1.58 fM obtained. This shows the great promise of our HCR-AgNCs nanosensor for clinical application.     

A new ultrafast and high-throughput mass spectrometric approach for the therapeutic drug monitoring of the multi-targeted anti-folate pemetrexed in plasma from lung cancer patients

An analytical assay has been developed and validated for ultrafast and high-throughput mass spectrometric determination of pemetrexed concentrations in plasma using matrix assisted laser desorption/ionization–triple quadrupole–tandem mass spectrometry. Patient plasma samples spiked with the internal standard methotrexate were measured by multiple reaction monitoring. The detection limit was 0.4 fmol/μL, lower limit of quantification was 0.9 fmol/μL, and upper limit of quantification was 60 fmol/μL, respectively. Overall observed pemetrexed concentrations in patient samples ranged between 8.7 (1.4) and 142.7 (20.3)?pmol/μL (SD). The newly developed mass spectrometric assay is applicable for (routine) therapeutic drug monitoring of pemetrexed concentrations in plasma from non-small cell lung cancer patients.     

An “off-on” fluorescent switch assay for microRNA using nonenzymatic ligation-rolling circle amplification

The authors describe a fluorometric switch assay for microRNA (miRNA). It is based on nonenzymatic ligation-rolling circle amplification (NELRCA). A click chemistry-mediated functionalized linear template was prepared by self-cycling. It is capable of forming a modified circular template (MLT) with a triazole linkage for amplified agent. MiRNA can recognize a binding region of the MLT, activates the NELRCA, and converts into rolling circle amplification products (RCPs). Subsequently, the added FAM-labeled signal probes (FAM-SPs) can hybridize to the RCPs. This RCPs/FAM-SPs duplex is less adsorbed onto the graphene oxide (GO) so that fluorescence (best measured at excitation/emission wavelengths of 490/520 nm) increases. In contrast to classical GO-based adsorption and displacement sensing system, the designed hybridization and adsorption fluorescent switch-on platform can reduce the assay time, and improve the detection efficiency of target. Under optimal conditions, the sensing platform has a detection limit as low as 0.75 fM. It can well discriminate target miRNA from other kinds of miRNA. Conceivably, this method can be extended to the trace detection of other nucleic acid biomarkers, and simultaneous recognition of multiple targets, thereby improving the early clinical diagnostic accuracy of cancer.

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Graphical abstract A hybridization and adsorption switch-on sensing system was fabricated on nonenzymatic ligation-rolling circle amplification. Modified circular template with 1,4-connect triazole linkage was adopted as an identified and amplified agent for high sensitive detection of microRNA.

     

High-throughput quantitative detection of triple-negative breast cancer-associated expressed miRNAs by rolling circle amplification on fluorescence-encoded microspheres

Compared with other types of breast cancer, triple-negative breast cancer(TNBC) has the characteristics of a high degree of malignancy and poor prognosis. Early diagnosis of TNBC through biological markers and timely development of effective treatment methods can reduce its mortality. Many Research experiments have confirmed that some specific mi RNA expression profiles in TNBC can used as markers for early diagnosis. However, detecting the expression profiles of multiple groups of miRNAs accord...     

Comparative microRNA detection from precursor-microRNA-transfected hepatocellular carcinoma cells by capillary electrophoresis with dual-color laser-induced fluorescence

A dual-LIF (dLIF) setup combined with CE for microRNA (miRNA) detection is proposed in this study. An argon ion laser (488 nm) and a solid state laser (640 nm) were chosen to excite the fluorescent dye-labeled DNA probe after splinted ligation of miRNA. The crosstalk of emission spectrum of Alex Fluor 488 and Alex Fluor 647 is minimized with a zero crosstalk matrix for Alex Fluor 647 to 488 channels. The linear ranges of the device for the fluorescent dye-labeled DNA probe were both from 1.0 nM to 0.1 pM. The limits of detection for Alexa Fluor 488-labeled DNA and Alex Fluor 647-labeled DNA were 9.3 and 31 fM, respectively. The detection of specific miRNA has been accomplished by combining splinted ligation with the fluorescent dye-labeled oligonucleotides. The linear range for the synthetic miRNA is from 1.0 nM to 1.0 pM. Without PCR amplification, CE-dLIF was applied to discriminate a pre-miR-10b*-transfected cells (contains precursor miR-10b*) from hepatocellular carcinoma cell (control cells). Therefore, this result indicates CE-dLIF has great potential to provide a rapid comparative assay for miRNAs detection.     

普鲁士蓝@石墨烯-壳聚糖纳米复合物用于构建microRNA电化学传感器的研究

制备了基于普鲁士蓝(PB)、石墨烯(GN)、壳聚糖(Chi)的纳米复合物(PB@GN-Chi),并将其修饰在玻碳电极表面制得microRNA电化学传感器。实验发现,GN可有效提高敏感膜的导电性能和比表面积,增强PB在电极表面的稳定性和传感器的重现性。通过戊二醛的交联作用,将氨基化的捕获探针(ssDNA)固载在PB@GN-Chi修饰的电极表面,并用于miR-21的检测。以透射电子显微镜对纳米复合物的形态进行表征,采用循环伏安法、示差脉冲伏安法对传感器的电化学特性进行研究。实验结果表明,该传感器具有良好的稳定性和重现性,在2.8~2.8×10~4pmol/L浓度范围内,响应电流与miR-21浓度的对数呈线性关系,检出限为0.87 pmol/L,可用于miR-21的检测。