Improving the Sensitivity of the miRNA Assay Coupled with the Mismatched Catalytic Hairpin Assembly Reaction by Optimization of Hairpin Annealing Conditions

Chemiluminescent heterogeneous and homogeneous-heterogeneous assays for determination of nicking endonuclease activity

Homogeneous-heterogeneous and heterogeneous formats of a simple and sensitive assay for the determination of nicking endonuclease (NE) Nt.Bst9I activity was developed. The duplex of two 26-membered biotinylated DNA oligonucleotides was used as a substrate of Nt.Bst9I. To improve the assay sensitivity the chemiluminescent detection system based on the use of conjugate of streptavidin and polyperoxidase and enhanced chemiluminescence reaction was used. Both proposed assay formats were constructed using microtiter plates as a solid support, allowing for easy automation of NE analysis using ELISA equipment. Varying the acidity, concentration of KCl and NaCl, and temperature of the reaction medium, favorable conditions were found. Although both formats of the proposed assay can be applied to estimate Nt.Bst9I activity, the heterogenous assay was more sensitive than the homogeneous-heterogeneous one.

Catalytic hairpin assembly triggering amplified DNAzyme-feedback for sensitive detection of hepatitis C virus genotype 1b

Developing a simple, reliable, and sensitive hepatitis C virus (HCV) genetic sensing platform is of great significance for diagnosing diseases and selecting appropriate antiviral treatments. Herein, a tandem nucleic acid amplification strategy for sensitive detection of HCV genotype 1b (HCV-1b) was developed by stringing the catalytic hairpin assembly (CHA) and the triggered DNAzyme amplifier. The hairpin reactants were initiated by the target to produce lots of triggering double-stranded DNA sequences which can efficiently activate the subsequent blocked DNAzyme. Thereby, the continuous cleavage of substrate was realized, resulting in the fluorescence signal amplification. The DNA-based isothermal CHA-DNAzyme (CDz) sensing platform was successfully applied for sensitive detection of HCV-1b with the limit of detection (84 pM) and showed good selectivity. Moreover, the practical detection of target DNA in the complex biologic matrix indicated that the developing strategy had good potential for early HCV infection diagnosis.

3D walkable DNA gears for ultrasensitive detection of multiple microRNAs in lung cancer cell lysates

As a tumor biomarker with therapeutic application potential, microRNA (miRNA) was crucial for the accurate and sensitive detection of early-stage tumors. Herein, a unique three dimensional (3D) DNA nanomachine (DNM) was created, which was capable detecting lung cancer-related biomarkers miRNA-21, miRNA-205 and miRNA-125b in lung cancer cell lysates with extreme sensitivity. The 3D DNM was composed of DNA scissors and three flexible walkable DNA gears modified with various species of silver nanoclusters (AgNCs). Based on the flexibility of DNA scissors and the walkability of DNA gears, neighboring DNA gears closed the distance between different species of AgNCs by walking in the presence of targets, generating fluorescence resonance energy transfer (FRET) effect and emitting different kinds of fluorescence to complete the highly sensitive detection of single targets and multiple targets. The findings demonstrated that a linear model provided an excellent match for the association between fluorescence signal and target miRNAs. For miRNA-21, miRNA-205, and miRNA-125b, the limits of detection (LODs) (signal/noise = 3) were 4.2 pmol/L (pM), 6.3 pM, and 10.2 pM, respectively. Their recoveries in A549 cell lysate samples ranged from 95.3 to 108.8 % with relative standard deviations of 1.26 %-4.88 %. Satisfactorily, the 3D DNM displayed exceptional analytical performance with high sensitivity and stability, strong specificity and reproducibility, which was triumphantly employed to identify miRNAs in tumor cell lysates, providing a workable technique in creating adaptable nanostructure for dependable bioanalysis and clinical diagnosis of cancer biomarkers.

Dual Signal Amplification by Urease Catalysis and Silver Nanoparticles for Ultrasensitive Colorimetric Detection of Nucleic Acids

Signal amplification techniques are highly desirable for the analysis of low-level targets that are closely related with diseases and the monitoring of important biological processes. However, it is still challenging to achieve this goal in a facile and economical way. Herein, we developed a novel dual signal amplification strategy by combining urease catalysis with the release of Ag⁺ from silver nanoparticles (AgNPs). This strategy was used for quantifying a DNA sequence (HIV-1) related with human immunodeficiency virus (HIV). DNA target HIV-1 hybridizes with the capture DNA probe on magnetic beads and the reporter DNA probe on AgNPs, forming a sandwich complex. The captured AgNPs are then transformed into numerous Ag⁺ ions that inactivate numerous ureases. Without catalytic production of ammonia from urea, the substrate solution shows a low pH 5.8 that will increase otherwise. The pH change is monitored by a pH indicator (phenol red), which allows for colorimetric detection. The proposed approach is sensitive, easy to use, economic, and universal, exhibiting a low detection limit of 9.7 fM (i.e., 1.94 attomoles) and a dynamic linear range of 4 orders for HIV-1 sequence detection.

Bidirectional motivated bimodal isothermal strand displacement amplifier with a table tennis-like movement for the ultrasensitive fluorescent and colorimetric detection of depression-related microRNA

An increasing number of studies have highlighted the potential of microRNAs (miRNAs) as physiological indicators of major depressive disorder (MDD). Herein, we developed a bidirectional-motivated bimodal isothermal strand displacement amplifier (BB-ISDA) for the ultrasensitive fluorescent and colorimetric detection of MDD-related miRNA-132. In the BB-ISDA system, a pair of functionalized hairpin probes (HP1 and HP2) with nicking recognition sites are designed to recognize target miRNA. The recognition of target miRNA by HP1 (or HP2) generates copious numbers of nicked triggers by HP1 (or HP2)-based ISDA to recognize HP2 (or HP1) by autonomous strand polymerization, cleavage, and displacement, which in turn induces the subsequent generation of copious numbers of nicked G-quadruplex triggers by HP2 (or HP1)-based ISDA to recognize HP1 (or HP2) along a same line. After many cycles, this bidirectional motivated table-tennis-like movement amplifies the fluorescent signal from HP1 and the colorimetric signal from HP2, simultaneously. The dual-signal output pattern was cross-validated for sensing miRNA-132. Each of the detection modal shows the capability for qualitative and quantitative detection of miRNA-132 with high sensitivity and specificity. The adaptability of the bimodal mechanism was verified via the detection of target miRNA-132 from clinical human blood samples. We envision that this BB-ISDA with dual-signal output for accurate and reliable analysis of miRNA is promising for the molecular diagnosis of human mental diseases.

A catalytic hairpin assembly-based Förster resonance energy transfer sensor for ratiometric detection of ochratoxin A in food samples

Ochratoxin A (OTA) poses severe risks to the environment and human health, making the development of an accurate and sensitive analytical method for OTA detection essential. In this study, a catalytic hairpin assembly (CHA)-based Förster resonance energy transfer (FRET) aptasensor was developed to detect OTA using carbon quantum dots (CDs) and 6-carboxy-fluorescein (FAM) as dual signal readout. In the presence of OTA, the aptamer specifically interacted with OTA to release the helper DNA (HP), which could open the hairpin structure of FAM-labeled hairpin DNA 1 (H₁-FAM) modified on the surface of gold nanoparticles (AuNPs). CHA between H₁-FAM and hairpin H₂ labeled with CDs (H₂-CDs) can release HP for the next cycle, resulting in the occurrence of FRET with CDs as the energy donor and FAM as the energy acceptor. According to the ratio of F_CDs/F_FAM, the proposed aptasensor showed a wide linear range from 5.0 pg/mL to 3.0 ng/mL and a low detection limit of 1.5 pg/mL for OTA detection. Moreover, satisfactory results were obtained for OTA detection in rice, suggesting the potential application of this sensor in food safety analysis.

Quantitation of MicroRNA-155 in Human Cells by Heterogeneous Enzyme-Linked Oligonucleotide Assay Coupled with Mismatched Catalytic Hairpin Assembly Reaction

In the present work, we describe the development of a chemiluminescent enzyme-linked oligonucleotide assay coupled with mismatched catalytic hairpin assembly (mCHA) amplification for the quantitative determination of microRNA-155. To improve its sensitivity, a polymerase-free mCHA reaction was applied as an isothermal amplification method. The detection limit of the proposed assay was 400 fM. In addition, the high specificity of the assay was demonstrated. The proposed assay allowed assessment of the content of microRNA-155 in human cancer lines such as HepG2, Caco2, MCF7, and HeLa. The quantitation of microRNA-155 was performed after purification of short RNAs (less than 200 nt) from cell lysates since a high matrix effect was observed without this pre-treatment. The results of the quantitative determination of the microRNA content in cells were normalized using nematode microRNA-39, the concentration of which was determined using a heterogeneous assay developed by us using a strategy identical to that of the microRNA-155 assay.

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.

DNA Logic Nanodevices for the Sequential Imaging of Cancer Markers through Localized Catalytic Hairpin Assembly Reaction

Monitoring tumor biomarkers is crucial for cancer diagnosis, progression monitoring, and treatment. However, identifying single or multiple biomarkers with the same spatial locations can cause false-positive feedback. Herein, we integrated the DNA tetrahedron (DT) structures with logic-responsive and signal amplifying capability to construct transmembrane DNA logic nanodevices (TDLNs) for the in situ sequential imaging of transmembrane glycoprotein mucin 1 (MUC1) and cytoplasmic microRNA-21 (miR-21) to cell identifications. The TDLNs were developed by encoding two metastable hairpin DNAs (namely, H1 and H2) in a DT scaffold, in which the triggering toeholds of H1 for miR-21 were sealed by the MUC1-specific aptamer (MUC1-apt). The TDLNs not only had the function of signal amplification owing to the localized catalytic hairpin assembly (CHA) reaction through spatial constraints effect of DT structures but also performed an AND logic operation to output a green Cy3 signal in MCF-7 cells, where MUC1 protein and miR-21 were simultaneously expressed. These results showed that the newly developed TDLNs have better molecular targeting and recognition ability so as to be easily identify cell types and diagnose cancer early.

Label- and enzyme-free plasmon-enhanced single molecule fluorescence detection of HIV DNA fragments based on a catalytic hairpin assembly

We developed a label- and enzyme-free single molecule fluorescence counting strategy for HIV DNA fragments detection. The nucleic acid biosensor consists of a 5' terminal connected with a triangular gold nanoplate, 3' terminal rich in guanine hairpin probe (HP1) and a hairpin probe HP2 complementary to the partial sequence of HP1. Without the existence of the target DNA, the DNA fragment rich in the guanine region is locked in a hairpin structure and cannot form a G-quadruplex, hence NMM exhibits a low fluorescence signal. When the target DNA exists, the hairpin assembly will trigger a strand displacement amplification reaction that produces a great number of G-quadruplexes, and the fluorescence brightness of NMM will be enhanced. The plasmon resonance effect of the triangular gold nanoplates will further amplify the fluorescence signal. This method can analyze the target DNA with high sensitivity and selectivity, and the detection limit is 0.83 fM. The analysis of the HIV DNA fragments in diluted human serum samples was successfully achieved, and the recovery rate was 92%-104%. Because of its easy operation and low cost, it has broad development potential in biochemical analysis and clinical applications.

Comparison of chemiluminescent heterogeneous and homogeneous–heterogeneous assays coupled with isothermal circular strand-displacement polymerization reaction amplification for the quantification of miRNA-141

A heterogeneous and homogeneous–heterogeneous chemiluminescent microplate assay was developed for the determination of miRNA-141 levels in human cells.

Photoactivated DNA Walker Based on DNA Nanoflares for Signal-Amplified MicroRNA Imaging in Single Living Cells

Specific and sensitive detection and imaging of cancer-related miRNA in living cells are desirable for cancer diagnosis and treatment. Because of the spatiotemporal variability of miRNA expression level during different cell cycles, signal amplification strategies that can be activated by external stimuli are required to image miRNAs on demand at desired times and selected locations. Herein, we develop a signal amplification strategy termed as the photoactivated DNA walker based on DNA nanoflares, which enables photocontrollable signal amplification imaging of cancer-related miRNA in single living cells. The developed method is achieved via combining photoactivated nucleic acid displacement reaction with the traditional exonuclease III (EXO III)-assisted DNA walker based on DNA nanoflares. This method is capable of on-demand activation of the DNA walker for dictated signal amplification imaging of cancer-related miRNA in single living cells. The developed method was demonstrated as a proof of concept to achieve photoactivated signal amplification imaging of miRNA-21 in single living HeLa cells via selective two-photon irradiation (λ = 740 nm) of single living HeLa cells by using confocal microscopy equipped with a femtosecond laser.

A label-free and signal-amplifiable assay method for colorimetric detection of carcinoembryonic antigen

In this work, an innovative colorimetric assay method for the determination of carcinoembryonic antigen is developed with aptamer probes utilized as recognition element. DNA hybridization chain reaction is used as signal amplification technique, and peroxidase-mimicking hemin/G-quadruplex-assisted catalytic oxidation of 2,2'-azino-bis-3-ethylbenzothiazoline-6-sulfonic acid (ABTS) is deployed as signal reporting mechanism. The detection principle was firstly verified by using gel electrophoresis analysis and absorbance measurements. After condition optimization, a detection limit was theoretically determined as 24.8 ng/ml. Furthermore, the method exhibited good selectivity and satisfactory recovery rates (92.2%-108.6%) in serum samples. Moreover, the sensing scheme is easily extended for the detection of other analytes via similar target-aptamer recognition principle. To sum up, this is an enzyme- and label-free, cost-effective yet signal-amplifiable assay scheme for the determination of tumor markers with promising simplicity and selectivity, practical utility, and potential universality.