Target-triggered hybridization chain reaction for ultrasensitive dual-signal miRNA detection

An electrochemical biosensor based on DNA tetrahedron nanoprobe for sensitive and selective detection of doxorubicin

Doxorubicin (DOX) is a clinical chemotherapeutic drug and patients usually suffer from dose-dependent cytotoxic and side effects during chemotherapy process with DOX. Therefore, developing a reliable strategy for DOX analysis in biological samples for dosage guidance during chemotherapy process is of great significance. Herein, a sensitive and selective electrochemical biosensor for DOX detection was designed based on gold nanoparticles (AuNPs) and DNA tetrahedron (TDN) nanoprobe bifunctional glassy carbon electrode that could detect DOX in human serum and cell lysate samples. AuNPs not only could enhance electron transfer efficiency and detection sensitivity, but also could improve the biocompatibility of electrode. TDN nanoprobes were employed as specific DOX bind sites that could bind abundant DOX through intercalative characteristics to contribute to sensitive and selective detection. Under the optimal conditions, the proposed TDN nanoprobes-based DOX biosensor exhibited a wide linear range that ranged from 1.0 nM to 50 μM and a low detection limit that was 0.3 nM. Moreover, the proposed DOX biosensor displayed nice selectivity, reproducibility and stability, and was successfully applied for DOX detection in human serum and cell lysate samples. These promising results maybe pave a way for DOX dosage guidance and therapeutic efficacy optimization in clinic.

Design and analysis of self-priming extension DNA hairpin probe for miRNA detection based on a unified dynamic programming framework

MicroRNAs (miRNAs) are potential biomarkers for cancer diagnosis and prognosis, methods for detecting miRNAs with high sensitivity, selectivity, and stability are urgently needed. Various nucleic acid probes that have traditionally been for this purpose suffer several drawbacks, including inefficient signal-to-noise ratios and intensities, high cost, and time-consuming method establishment. Computing tools used for investigating the thermodynamics of DNA hybridization reactions can accurately predict the secondary structure of DNA and the interactions between DNA molecules. Herein, NUPACK was used to design a series of nucleic acid probes and develop a phosphorothioated-terminal hairpin formation and self-priming extension (PS-THSP) signal amplification strategy, which enabled the ultrasensitive detection of miR-200a in serum samples. The free and binding energies of the DNA detection probes calculated using NUPACK, as well as the biological experimental results, were considered synthetically to select the best sequence and experimental conditions. A unified dynamic programming framework, NUPACK analysis and the experimental data, were complementary and improved the designed model in all respects. Our study demonstrates the feasibility of using computer technology such as NUPACK to simplify the experimental process and provide intuitive results.

A dual-signal amplification strategy based on rolling circle amplification and APE1-assisted amplification for highly sensitive and specific miRNA analysis for early diagnosis of alzheimer's disease

MicroRNA (miRNA) is involved in the progression of Alzheimer's disease (AD) and emerges as a promising AD biomarker and therapeutic target. Therefore, there is an urgent need to develop convenient and precise miRNA detection methods for AD diagnosis. Herein, a dual-signal amplification strategy based on rolling circle amplification and APE1-assisted amplification for miRNA analysis for early diagnosis of AD was proposed. The strategy consisted of dumbbell-shaped probe (DP) as amplification template and a reporter probe (RP) with an AP site modification. In the presence of the target miRNA, the miRNAs bound to the toehold domain of DP and DP was activated into a circular template. Then, RCA reaction was triggered, producing a large number of long-stranded products containing repeated sequences. After RCA, APE1 enzyme recognized and removed AP site in the complex of RCA/RP products. By coupling RCA with APE1-assisted amplification, this method has high sensitivity with the limit of detection (LOD) of 1.82 fM. Moreover, by using DP as template for RCA reaction, high specificity can be achieved. By detecting miR-206 in serum using this method, the expression of miR-206 can be accurately distinguished between AD patients and healthy individuals, indicating that this method has broad application prospects in clinical diagnosis.

CRISPR-Cas13a-Triggered DNAzyme Signal Amplification-Based Colorimetric miRNA Detection Method and Its Application in Evaluating the Anxiety

The development of a bio-sensing strategy based on CRISPR/Cas that is exceptionally sensitive is crucial for the identification of trace molecules. Colorimetric miRNA detection utilizing CRISPR/Cas13a-triggered DNAzyme signal amplification was described in this article. The developed strategy was implemented for miRNA-21 detection as a proof of concept. The cleavage activity of Cas13a was triggered when the target molecule bonded to the Cas13a-crRNA complex and cleaved uracil ribonucleotides (rU) in the substrate probe. As a consequence, the S chain was liberated from the T chain that had been modified on magnetic beads (MB). The G-rich sections were then exposed when the catalytic hairpin assembly between the H1 and H2 probes was activated by the released T@MB. G-rich section can fold into G-quadruplex. By catalyzing the formation of green ABTS3- via HRP-mimicking G-quadruplex/hemin complexes, colorimetric measurements of miRNA can be achieved visually through DNAzyme-mediated signal amplification. The method demonstrated a low limit of detection of 27 fM and a high selectivity towards target miRNA eventually. As a result, the developed strategy provides a clinical application platform for the detection of miRNAs that is both ultrasensitive and extremely specific.

DNAzyme amplified dispersion state change of gold nanoparticles and its dual optical channels for ultrasensitive and facile detection of lead ion in preserved eggs

A dual-mode sensing platform for Pb2+ was constructed based on the dual optical channels of Au NPs system with the amplification of DNAzyme, and it was successfully applied for Pb2+ determination in preserved egg with satisfactory results. The presence of Pb2+ activated the DNAzyme and induced the dispersion change of Au NPs in high salt concentration. The sequent absorption change of Au NPs was translated to the fluorescence change of carbon dots through FRET, and the scattering change was transferred to grey value of images involving the Tyndall effect. Thus, a sensing platform based on fluorescence and colorimetric dual-technique was achieved for Pb2+ detection, under the optimized conditions. With the assistance of DNAzyme, the linear range of fluorometric and colorimetric method were 2.0 × 10-14 ∼ 8.0 × 10-10 mol/L and 2.4 × 10-13 ∼ 9.5 × 10-9 mol/L, respectively. The dual-mode sensing platform demonstrated its promising application in the environmental monitoring and food safety field.

A two-step electrochemical biosensor based on Tetrazyme for the detection of fibrin

In this study, an electrochemical biosensor was constructed for the detection of fibrin, specifically by a simple two-step approach, with a novel artificial enzyme (Tetrazyme) based on the DNA tetrahedral framework as signal probe. The multichannel screen-printed electrode with the activated surface cannot only remove some biological impurities, but also serve as a carrier to immobilize a large number of antigen proteins. The DNA tetrahedral nanostructure was employed to ensure the high sensitivity of the probe for biological analysis. The hemin was chimeric into the G-quadruplex to constitute the complex with peroxidase catalytic activity (hemin/G4-DNAzyme), subsequently, Tetrazyme was formed through combining of this complex and DNA tetrahedral nucleic acid framework. The artificial enzyme signal probe formed by the covalent combination of the homing peptide (Cys-Arg-Glu-Lys-Ala, CREKA), which is the aptamer of fibrin and the new artificial enzyme is fixed on the surface of the multichannel carbon electrode by CREKA-specific recognition, so as to realize the sensitive detection of fibrin. The feasibility of sensing platform was validated by cyclic voltammetry (CV) and amperometric i-t curve (IT) methods. Effects of Tetrazyme concentration, CREKA concentrations and hybridization time on the sensor were explored. Under the best optimal conditions of 0.6 μmol/L Tetrazyme, 80 μmol/L CREKA, and 2.5 h reaction time, the immunosensor had two linear detection ranges, 10-40 nmol/L, with linear regression equation Y = 0.01487X - 0.011 (R2 = 0.992), and 50-100 nmol/L, with linear regression equation Y = 0.00137X + 0.6405 (R2 = 0.998), the detection limit was 9.4 nmol/L, S/N ≥ 3. The biosensor could provide a new method with great potential for the detection of fibrin with good selectivity, stability, and reproducibility.

Electrochemical nucleic acid sensors: Competent pathways for mobile molecular diagnostics

Electrochemical nucleic acid biosensor has demonstrated great promise in clinical diagnostic tests, mainly because of its flexibility, high efficiency, low cost, and easy integration for analytical applications. Numerous nucleic acid hybridization-based strategies have been developed for the design and construction of novel electrochemical biosensors for diagnosing genetic-related diseases. This review describes the advances, challenges, and prospects of electrochemical nucleic acid biosensors for mobile molecular diagnosis. Specifically, the basic principles, sensing elements, applications in diagnosis of cancer and infectious diseases, integration with microfluidic technology and commercialization are mainly included in this review, aiming to provide new insights and directions for the future development of electrochemical nucleic acid biosensors.

miRNA Detection for Prostate Cancer Diagnosis by miRoll-Cas: miRNA Rolling Circle Transcription for CRISPR-Cas Assay

Micro-RNA (miRNA) emerges as a promising type of biomarker for cancer diagnosis. There is an urgent need for developing rapid, convenient, and precise miRNA detection methods that may be conducted with limited laboratory facilities, especially in underdeveloped areas. Herein, we developed a miRNA detection method termed miRoll-Cas, where miRNA is first amplified by rolling circle transcription and then subject to CRISPR-Cas13a assay. Using miRoll-Cas, we realized the sensitive detection of multiple cancer-relevant miRNA markers (miR21, miR141, and Let7b) and specifically identified other variants of the Let7 family, which can accurately discriminate prostate cancer patients from healthy people. We envision that miRoll-Cas may be readily translated to clinical applications in the diagnosis of a variety of diseases beyond cancer.

Hybridization chain reaction cascaded amplification platform for sensitive detection of pathogen

Rapid, sensitive, and accurate identification of pathogens is vital for preventing and controlling fish disease, reducing economic losses in aquaculture, and interrupting the spread of food-borne diseases in human populations. Herein, we proposed a hybridization chain reaction (HCR) cascaded dual-signal amplification platform for the ultrasensitive and specific detection of pathogenic microorganisms. A couple of specific primers for target bacterial 16S rRNAs were used to obtain amplified target single-stranded DNAs (AT-ssDNA). Then, AT-ssDNA initiated HCR amplification along with the opening of fluorophore (FAM) and a quencher (BHQ1) labeled hairpin reporter probe (H1), and the FAM fluorescence signal recovered. The proposed strategy could achieve a detection limit down to 0.31 CFU/mL for Staphylococcus aureus (S. aureus), 0.49 CFU/mL for Escherichia coli (E. coli) in buffer, and a linear range from 1 to 1 × 10⁶ CFU/mL for S. aureus, 1 to 1 × 10⁷ CFU/mL for E. coli. Furthermore, this platform enabled sensitive and precise detection of pathogenic microorganisms in complex samples such as fish blood and different organ tissues (large intestine, gallbladder, heart, liver, ren, gill, skin), which shows great potential in disease prevention and control in aquatic products.

Polyhedral Au Nanoparticle/MoOx Heterojunction-Enhanced Ultrasensitive Dual-Mode Biosensor for miRNA Detection Combined with a Nonenzymatic Cascade DNA Amplification Circuit

A novel homologous surface-enhanced Raman scattering (SERS)-electrochemical (EC) dual-mode biosensor based on a 3D/2D polyhedral Au nanoparticle/MoO_x nanosheet heterojunction (PAMS HJ) and target-triggered nonenzyme cascade autocatalytic DNA amplification (CADA) circuit was constructed for highly sensitive detection of microRNA (miRNA). Mixed-dimensional heterostructures were prepared by in situ growth of polyhedral Au nanoparticles (PANPs) on the surface of MoO_x nanosheets (MoO_x NSs) via a seed-mediated growth method. As a detection substrate, the resulting PAMS HJ shows the synergistic effects of both electromagnetic and chemical enhancements, efficient charge transfer, and robust stability, thus achieving a high SERS enhancement factor (EF) of 4.2 × 10⁹ and strong EC sensing performance. Furthermore, the highly efficient molecular recognition between the target and smart lock probe and the gradually accelerated cascade amplification reaction further improved the selectivity and sensitivity of our sensing platform. The detection limits of miRNA-21 in SERS mode and EC mode were 0.22 and 2.69 aM, respectively. More importantly, the proposed dual-mode detection platform displayed excellent anti-interference and accuracy in the analysis of miRNA-21 in human serum and cell lysates, indicating its potential as a reliable tool in the field of biosensing and clinical analysis.

A Novel Electrochemical Sensing Strategy Based on Poly (3, 4-ethylenedioxythiophene): Polystyrene Sulfonate, AuNPs, and Ag+ for Highly Sensitive Detection of Alkaline Phosphatase

Alkaline phosphatase (ALP) is a crucial marker for the clinical analysis and detection of many diseases. In this study, an accurate signal amplification strategy was proposed for the sensing and quantification of alkaline phosphatase using poly (3, 4-ethylenedioxythiophene):polystyrene sulfonate (PEDOT:PSS), gold nanoparticles (AuNPs), and Ag⁺. Signal amplification was achieved by the modification of PEDOT:PSS and AuNPs on glassy carbon electrodes. Atomic force microscopy was performed to characterize the morphology of the modified nanomaterials. To detect ALP, 1-naphthyl phosphate (1-NP) was used as the substrate, and alkaline phosphatase catalyzed 1-NP into 1-naphthol (1-N), which resulted in the reduction of Ag⁺ to Ag⁰ on the surface of the modified electrode (AuNPs/PEDOT:PSS/GCE). The deposition of Ag drastically enhanced the detection signal. Differential pulse voltammograms of 1-N, which is the enzymatic product from the ALP reaction with 1-NP, were recorded. In the linear range of 0.1-120 U L^-1, a quantitative analysis of alkaline phosphatase was achieved, with high sensitivity and a low detection limit of 0.03 U L^-1. Stable, selective, and reproducible electrochemical sensors were designed. Moreover, the proposed electrochemical sensor exhibited a prominent sensing performance in the spiked diluted human serum. Thus, the sensor can be used in numerous applications in alkaline phosphatase or other analyte detection.