Dual-output toehold-mediated strand displacement amplification for sensitive homogeneous electrochemical detection of specie-specific DNA sequences for species identification

A novel entropy-driven dual-output mode integrated with DNAzyme for enhanced microRNA detection

Accurate microRNA (miRNA) detection is pivotal in the diagnosis and monitoring of cancer. Entropy-driven catalysis (EDC) has attracted widespread attention as an enzyme-free, isothermal technique for miRNA detection owing to its inherent simplicity and reliability. However, conventional EDC is a single-output mode, limiting the efficiency of signal amplification. In this study, a novel EDC dual-output mode was employed in conjunction with DNAzyme, resulting in the development of an EDC dual-end DNAzyme (EDC-DED) approach for highly sensitive miRNA detection. In this system, miRNA-21 initiated the EDC reaction, producing a large amount of catalytically active dual-end Mg2+-dependent DNAzyme. The DNAzyme further cleaved the reporter cyclically, generating a notably amplified fluorescence signal. The proposed method achieved a low detection limit of 2 pM. Compared with the traditional EDC single-end DNAzyme (EDC-SED) strategy, the present method exhibited superior amplification efficiency, enhancing detection sensitivity by approximately 46.5-fold. Furthermore, this platform demonstrated ideal specificity, satisfactory reproducibility and acceptable detection capabilities in clinical serum samples. Therefore, the straightforward and convenient strategy is a potential tool for miRNA analysis, which may provide a new perspective for biological analysis and clinical application.

Cascade signal amplification strategy for the electrochemical aptasensing of nucleic acid: Combination of dual-output toehold-mediated DNA strand displacement, DNA walker and Exo III

BACKGROUND

Sensitive and selective analysis of low content nucleic acid sequences plays an important role in pathogen analysis, disease diagnosis and biomedicine. The electrochemical biosensor based on toehold-mediated strand displacement reaction (TMSD) is highly attractive in nucleic acid detection due to their improved sensitivity and rapid response. But the traditional TMSD carried out on the electrode always with low displacement efficiency and complicated electrode operation, resulting in compromised sensing performance. There is a great need to construct a novel TMSD based electrochemical detection strategy to overcome such challenges in nucleic acid detecting.

RESULT

Herein, a triple signal amplification electrochemical aptasensor was developed for ultrasensitive detection of CYFRA21-1 DNA. The dual-output toehold mediated strand displacement reaction (dTMSD) can convert one input to two strands output within one strand displacement cycle. So that it possesses a higher efficiency for improving the sensitivity in comparison with the single-output TMSD. And the fuel strand was configured with a tail to realize successive DNA circuits through self-propelling as a DNA walker. All the above processes were carried out on magnetic beads, which is conducive to achieving effective sample purification and minimizing the background signals. Besides, Exonuclease III was further amplified signal. As a result, through the cascade use of above three technologies, the proposed biosensing strategy realized sensitive detection of target DNA with a low detection limit of 0.35 fM (S/N = 3) and wide linear range (0.5 fM-500 pM).

SIGNIFICANCE

The proposed novel dTMSD combining multiple signal amplification strategies for electrochemical detection of CYFRA21-1 DNA with easy operation not only possesses excellent sensitivity and selectivity, but also has potential application value for monitoring DNA in serum. Meanwhile, the development of highly sensitive and specific CYFRA21-1 DNA detection methods is very important for the prevention and treatment of lung cancer.

MicroRNA biosensors in lung cancer

Lung cancer has been one of the leading causes of death over the past century. Unfortunately, the reliance on conventional methods to diagnose the phenotypic properties of tumors hinders early-stage cancer diagnosis. However, recent advancements in identifying disease-specific nucleotide biomarkers, particularly microRNAs, have brought us closer to early-stage detection. The roles of miR-155, miR-197, and miR-182 have been established in stage I lung cancer. Recent progress in synthesizing nanomaterials with higher conductivity has enhanced the diagnostic sensitivity of electrochemical biosensors, which can detect low concentrations of targeted biomarkers. Therefore, this review article focuses on exploring electrochemical biosensors based on microRNA in lung cancer.

In situ reduction of gold nanoparticles-decorated MXenes-based electrochemical sensing platform for KRAS gene detection

In this work, gold nanoparticles@Ti3C2 MXenes nanocomposites with excellent properties were combined with toehold-mediated DNA strand displacement reaction to construct an electrochemical circulating tumor DNA biosensor. The gold nanoparticles were synthesized in situ on the surface of Ti3C2 MXenes as a reducing and stabilizing agent. The good electrical conductivity of the gold nanoparticles@Ti3C2 MXenes composite and the nucleic acid amplification strategy of enzyme-free toehold-mediated DNA strand displacement reaction can be used to efficiently and specifically detect the non-small cell cancer biomarker circulating tumor DNA KRAS gene. The biosensor has a linear detection range of 10 fM −10 nM and a detection limit of 0.38 fM, and also efficiently distinguishes single base mismatched DNA sequences. The biosensor has been successfully used for the sensitive detection of KRAS gene G12D, which has excellent potential for clinical analysis and provides a new idea for the preparation of novel MXenes-based two-dimensional composites and their application in electrochemical DNA biosensors.

A Versatile Electrochemical Biosensor for the Detection of Circulating MicroRNA toward Non-Small Cell Lung Cancer Diagnosis

Circulating microRNAs (miRNAs) can be used as noninvasive biomarkers and are also found circulating in body fluids such as blood. Dysregulated miRNA expression is associated with many diseases, including non-small cell lung cancer (NSCLC), and the miRNA assay is helpful in cancer diagnosis, prognosis, and monitoring. In this work, a versatile electrochemical biosensing system is developed for miRNA detection by DNAzyme-cleavage cycling amplification and hybridization chain reaction (HCR) amplification. With cleavage by Mn²⁺ targeted DNAzyme, DNA-walker can move along the predesigned DNA tracks and contribute to the transduction and enhancement of signals. For the electrochemical process, the formation of multiple G-quadruplex-incorporated long double-stranded DNA (dsDNA/G-quadruplex) structures is triggered through HCR amplification. The introduction of G-quadruplex allows sensitive measurement of miRNA down to 5.68 fM with good specificity. Furthermore, by profiling miRNA in the NSCLC cohort, this designed strategy shows high efficiency (area under the curve (AUC) of 0.879 using receiver operating characteristic (ROC) analysis) with the sensitivity of 80.0% for NSCLC early diagnosis (stage I). For the discrimination of NSCLC and benign disease, the assay displays an AUC of 0.907, superior to six clinically-acceptable protein tumor markers. Therefore, this platform holds promise in clinical application toward NSCLC diagnosis and prognosis.

A novel electrochemical biosensor for lung cancer-related gene detection based on copper ferrite-enhanced photoinitiated chain-growth amplification

We reported an electrochemical biosensor via CuFe₂O₄-enhanced photoinitiated chain-growth polymerization for ultrasensitive detection of lung cancer-related gene. In this work, photoinitiated atom transfer radical polymerization (ATRP) was applied to amplify the electrochemical signal corresponding to lung cancer-related gene, and polymerization was triggered off under the illumination of blue light which was involved in copper-mediated reductive quenching cycle. At the same time, CuFe₂O₄-H₂O₂ system was also activated to enhance polymerization based on the photocatalysis of CuFe₂O₄, which was based on the reaction between •OH and methacrylic monomers to generate carbon-based radicals. Numerous ferrocene-based polymer was graft onto electrode surface through this amplification stages. The limit of detection was low to 1.98 aM (in 10 μL, ∼11.9 molecules) (R² = 0.998) with a wide linear range from 0.1 fM to 10 pM. This strategy made a good trade-off between cost-effectiveness and sensitivity, and it also presented a high selectivity and anti-interference. In addition, the operation was greatly simplified and detection time was also shortened, which endowed this electrochemical DNA biosensor great application potential.

Electrochemiluminescence Biosensor Based on Entropy-Driven Amplification and a Tetrahedral DNA Nanostructure for miRNA-133a Detection

The early and rapid diagnosis of acute myocardial infarction (AMI) is of great significance to its treatment. Here, we developed an electrochemiluminescence biosensor based on an entropy-driven strand displacement reaction (ETSD) and a tetrahedral DNA nanostructure (TDN) for the detection of the potential AMI biomarker microRNA-133a. In the presence of the target, numerous Ru(bpy)₃²⁺-labeled signal probes (SP) were released from the preformed three-strand complexes through the process of ETSD. The ETSD reaction cycle greatly amplified the input signal of the target. The released SP could be captured by the TDN-engineered biosensing interface to generate a strong ECL signal. The rigid structure of TDN could significantly improve the hybridization efficiency. With the assistant of double amplification of TDN and ETSD, the developed biosensor has a good linear response ranging from 1 fM to 1 nM for microRNA-133a, and the detection limit is 0.33 fM. Additionally, the constructed biosensor has excellent repeatability and selectivity, demonstrating that the biosensor possesses a great application prospect in clinical diagnosis.

Engineering a high-efficient DNA amplifier for biosensing application based on perylene decorated Ag microflowers as novel electrochemiluminescence indicators

DNA-based amplifiers with high programmability and accurate molecular recognition ability have become a versatile platform for target amplification. However, the random diffusion of capture probes (CPs) in most DNA amplifiers limits the target recognition efficiency, affecting the limit of detection. Herein, a high-efficient DNA amplifier was developed by localizing the CPs consisted of the unique palindromic tails and target recognition sequences on Au nanoparticle modified magnetic beads (Au@MBs). In the presence of target K-ras gene, the CPs with high local concentration and orientation could capture the target efficiently to expose their palindromic tails, which could act as primers to trigger the polymerization for target recycling. More importantly, the polymerization products could involve in the next recycle and produce abundant mimic targets (MTs) continuously, thereby achieving the detection of trace K-ras gene. Meanwhile, a novel electrochemiluminescence (ECL) indicator of a thin-layer of perylene (Pe) molecules decorated Ag microflowers (Pe@Ag MFs) was obtained based on the reaction between the perylene cation radical (Pe^•+) and Ag atoms. The obtained Pe@Ag MFs exhibited desirable ECL performance because (i) a thin-layer of Pe molecules could reduce the inner filter effect and inactive emitters, (ii) the Ag MFs as coreaction accelerator could react with S₂O₈^2- to produce more SO₄^•- and shorten the distance between Pe^•- and SO₄^•- to significantly enhance the ECL intensity of Pe with less energy loss. This work paves the way for the development of efficient amplification strategy and offers a paradigm for the preparation of high-efficiency ECL indicators.

Short DNA-catalyzed formation of quantum dot-DNA hydrogel for enzyme-free femtomolar specific DNA assay

Fast, sensitive, specific, and user-friendly DNA assay is a key technique for the next generation point-of-care molecular diagnosis. However, high-cost, time-consuming, and complicated enzyme-based DNA amplification step is essential to achieve high sensitivity. Herein, a short target DNA-catalyzed formation of quantum dot (QD)-DNA hydrogel is proposed as a new DNA assay platform satisfying the above requirements. A single-stranded target DNA catalyzes the opening cycle of DNA hairpin loops, which are quickly self-assembled with DNA-functionalized QDs to generate QD-DNA hydrogel. The three-dimensional hydrogel network allows efficient resonance energy transfer, dramatically lowering the limit of detection down to ~6 fM without enzymatic DNA amplification. The QD-DNA hydrogel also enables a rapid detection (1 h) with high specificity even for a single-base mismatch. The clinical applicability of the QD-DNA hydrogel is demonstrated for the Klebsiella pneumoniae carbapenemase gene, one of the key targets of drug-resistant pathogenic bacteria.

An amplifying DNA circuit coupled with Mg2+-dependent DNAzyme for bisphenol A detection in milk samples

As bisphenol A (BPA) is harmful to human health, it is of great significance to develop a new method for BPA detection. Herein, we designed a BPA biosensor by integrating an amplifying DNA circuit with Mg²⁺-dependent DNAzyme into the sensing system. The BPA-aptamer binding activated a DNA circuit for signal amplification based on toehold-mediated strand displacement. A catalytic Mg²⁺-dependent DNAzyme was formed through synergistically DNA hybridization, which can cleave the dual-labeled substrate DNA into two segments. The separation of the fluorophore and quencher produces a high fluorescence response for BPA detection. This biosensor exhibited a superior sensitivity with a detection limit of 50 fM. The method is selective and robust, which can work even in milk samples with satisfactory accuracy. The biosensor analytical results were also verified by liquid chromatography coupled with mass spectrometry (LC-MS) and no obvious difference existed between the two methods.

Electrochemical DNA Sensor for Sensitive BRCA1 Detection Based on DNA Tetrahedral-Structured Probe and Poly-Adenine Mediated Gold Nanoparticles

BRCA1 is the biomarker for the early diagnosis of breast cancer. Detection of BRCA1 has great significance for the genetic analysis, early diagnosis and clinical treatment of breast cancer. In this work, we developed a simple electrochemical DNA sensor based on a DNA tetrahedral-structured probe (TSP) and poly-adenine (polyA) mediated gold nanoparticles (AuNPs) for the sensitive detection of BRCA1. A thiol-modified TSP was used as the scaffold on the surface of the screen-printed AuNPs electrode. The capture DNA (TSP) and reporter DNA were hybridized to the target DNA (BRCA1), respectively, to form the typical sandwich system. The nanocomposites of reporter DNA (polyA at the 5′ end) combined with AuNPs were employed for signal amplification which can capture multiple enzymes by the specificity between biotin and streptavidin. Measurements were completed in the electrochemical workstation by cyclic voltammetry and amperometry and we obtained the low limit of detection of 0.1 fM with the linear range from 1 fM to 1 nM. High sensitivity and good specificity of the proposed electrochemical DNA sensor showed potential applications in clinical early diagnosis for breast cancer.