Exonuclease III-Powered Self-Propelled DNA Machine for Distinctly Amplified Detection of Nucleic Acid and Protein

A simple and sensitive colorimetric approach for mecA gene analysis via exonuclease-III catalyzed signal cascade

Analysis of mecA gene in Staphylococcus aureus (S. aureus) is essential for controlling infections in intensive care units (ICU) and preventing the use of ineffectual empirical treatments. However, quantitative determination of the mecA gene remains difficult. Herein, we propose a simple and sensitive colorimetric approach by integrating exonuclease-III (Exo-III) assisted signal cascade and G-quadruplex/hemin DNAzymes (G4 DNAzymes) catalyzed 2,2'-azino-bis (3-ethylben-zothiazoline-6-sulfonic acid) (ABTS) based color reaction. In this method, signal amplification does not necessitate the use of complex experimental components, such as multiple enzymes and primer design, while still maintaining a high signal amplifying efficiency. Therefore, the method has a broad mecA gene detection range from 10 fM to 1 nM and a low limit of detection down to 3.4 fM level. Taking the merit of simplicity and high sensitivity, the approach is promising in analyzing mecA gene in S. aureus and diagnosing infections.

Electrochemical aptasensor based on DNA-templated copper nanoparticles and RecJf exonuclease-assisted target recycling for lipopolysaccharide detection

An electrochemical aptasensor for detecting lipopolysaccharides (LPS) was fabricated based on DNA-templated copper nanoparticles (DNA-CuNPs) and RecJf exonuclease-assisted target recycling. The DNA-CuNPs were synthesized on a double-stranded DNA template generated through the hybridization of the LPS aptamer and its complementary chain (cDNA). In the absence of LPS, the CuNPs were synthesized on DNA double-strands, and a strong readout corresponding to the CuNPs was achieved at 0.10 V (vs. SCE). In the presence of LPS, the fabricated aptamer could detach from the DNA double-strand to form a complex with LPS, disrupting the template for the synthesis of CuNPs on the electrode. Meanwhile, RecJf exonuclease could hydrolyze the cDNA together with this single-stranded aptamer, releasing the LPS for the next round of aptamer binding, thereby enabling target recycling amplification. As a result, the electrochemical signal decreased and could be used to indicate the LPS content. The fabricated electrochemical aptasensor exhibited an extensive dynamic working range of 0.01 pg mL-1 to 100 ng mL-1, and its detection limit was 6.8 fg mL-1. The aptasensor also exhibited high selectivity and excellent reproducibility. Moreover, the proposed aptasensor could be used in practical applications for the detection of LPS in human serum samples.

Thermus thermophilus Argonaute-based signal amplifier for highly sensitive and specific microRNA detection

The prokaryote-derived gene defense system as a new generation of nucleic acid detection tool exhibits impressive performance in the field of molecular diagnosis. Prokaryotic Argonaute (Ago) is a CRISPR-associated protein that is guided by a short DNA (gDNA) and then efficiently cleaves gDNA-complementary nucleic acids and presents unique characteristics that are different from the CRISPR/Cas system. However, the application of Ago in biosensing is still relatively scarce, and many properties of Ago need to be further clarified. In this study, we aim to systematically explore the properties of Thermus thermophilus Argonaute (TtAgo), including the dependence of TtAgo activity on guide DNA (gDNA) length, substrates' length, and the position of gDNA complementary region on the substrate. Based on these properties, we constructed an exonuclease III-assisted target-recycled amplification system (exoAgo) for sensitive miRNA detection. The result showed that exoAgo can be used for miRNA profiling with a detection limit of 12.2 pM and single-base-resolution and keep good performance for the detection of complex samples, which indicates that Ago has great application potential in the detection of nucleic acids. In conclusion, this study will provide guidance for further development and utilization of Ago in the field of biosensing.

Electrochemical biomimetic enzyme cascade amplification combined with target-induced DNA walker for detection of thrombin

Fe-N-doped carbon nanomaterials (Fe-N/CMs) were designed as a novel biomimetic enzyme with excellent peroxidase-like activity to achieve high-efficient enzyme cascade catalytic amplification with the aid of glucose oxidase (GOx), which was further combined with target-induced DNA walker amplification to develop a sensitive electrochemical biosensor for thrombin detection. Impressively, massive output DNA was transformed from small amounts of target thrombin by highly effective DNA walker amplification as protein-converting strategy, which could then induce the immobilization of functionalized nanozyme on the electrode surface to achieve the high-efficient electrochemical biomimetic enzyme cascade amplification. As a result, an amplified enzyme cascade catalytic signal was measured for thrombin detection ranging from 0.01 pM to 1 nM with a low detection limit of 3 fM. Importantly, the new biomimetic enzyme cascade reaction coupled the advantages of natural enzyme and nanozyme, which paved an avenue to construct varied artificial multienzymes amplification systems for biosensing, bioanalysis, and disease diagnosis applications.

Multifunctional Exo III-assisted scalability strategy for constructing DNA molecular logic circuits

The construction of logic circuits is critical to DNA computing. Simple and effective scalability methods have been the focus of attention in various fields related to constructing logic circuits. We propose a double-stranded separation (DSS) strategy to facilitate the construction of complex circuits. The strategy combines toehold-mediated strand displacement with exonuclease III (Exo III), which is a multifunctional nuclease. Exo III can quickly recognize an apurinic/apyrimidinic (AP) site. DNA oligos with an AP site can generate an output signal by the strand displacement reaction. However, in contrast to traditional strand displacement reactions, the double-stranded waste from the strand displacement can be further hydrolysed by the endonuclease function of Exo III, thus generating an additional output signal. The DSS strategy allows for the effective scalability of molecular logic circuits, enabling multiple logic computing capabilities simultaneously. In addition, we succeeded in constructing a logic circuit with dual logic functions that provides foundations for more complex circuits in the future and has a broad scope for development in logic computing, biosensing, and nanomachines.

Palindrome-Embedded Hairpin Structure and Its Target-Catalyzed Padlock Cyclization for Label-Free MicroRNA-Initiated Rolling Circle Amplification

Highly sensitive detection of microRNAs (miRNAs) is of great significance in early diagnosis of cancers. Here, we develop a palindrome-embedded hairpin structure and its target-catalyzed padlock cyclization for rolling circle amplification, named PHP-RCA for simplicity, which can be applied in label-free ultrasensitive detection of miRNA. PHP-RCA is a facile system that consists of only an oligonucleotide probe with a palindrome-embedded hairpin structure (PHP). The two ends of PHP were extended as overhangs and designed with the complementary sequences of the target. Hence, the phosphorylated PHP can be cyclized by T4 DNA ligase in the presence of the target that serves as the ligation template. This ligation has formed a palindrome-embedded dumbbell-shaped probe (PDP) that allows phi29 polymerase to perform a typical target-primed RCA on PDP by taking miRNA as a primer, resulting in the production of a lengthy tandem repeat. Benefits from the palindromic sequences and hairpin-shaped structure in padlock double-stranded structures can be infinitely produced during the RCA reaction and provide numerous binding sites for SYBR Green I, a double-stranded dye, achieving a sharp response signal for label-free target detection. We have demonstrated that the proposed system exhibits a good linear range from 0.1 fM to 5 nM with a low detection limit of 0.1 fM, and the non-target miRNA can be clearly distinguished. The advantages of high efficiency, label-free signaling, and the use of only one oligonucleotide component make the PHP-RCA suitable for ultrasensitive, economic, and convenient detection of target miRNAs. This simple and powerful system is expected to provide a promising platform for tumor diagnosis, prognosis, and therapy.

Sensitive Interrogation of Enhancer Activity in Living Cells on a Nanoelectroporation-Probing Platform

Enhancers involved in the upregulation of multiple oncogenes play a fundamental role in tumorigenesis and immortalization. Exploring the activity of enhancers in living cells has emerged as a critical path to a deep understanding of cancer properties, further providing important clues to targeted therapy. However, identifying enhancer activity in living cells is challenging due to the double biological barriers of a cell cytoplasmic membrane and a nuclear membrane, limiting the sensitivity and responsiveness of conventional probing methods. In this work, we developed a nanoelectroporation-probing (NP) platform, which enables intranuclear probe delivery for sensitive interrogation of enhancer activity in living cells. The nanoelectroporation biochip achieved highly focused perforation of the cell cytoplasmic membrane and brought about additional driving force to expedite the delivery of probes into the nucleus. The probes targeting enhancer activity (named "PH probe") are programmed with a cyclic amplification strategy and enable an increase in the fluorescence signals over 100-fold within 1 h. The platform was leveraged to detect the activity of CCAT1 enhancers (CCAT1, colon cancer-associated transcript-1, a long noncoding RNA that functions in tumor invasion and metastasis) in cell samples from clinical lung cancer patients, as well as reveal the heterogeneity of enhancers among different patients. The observations may extend the linkages between enhancers and cancer cells while validating the robustness and reliability of the platform for the assay of enhancer activity. This platform will be a promising toolbox with wide applicable potential for the intranuclear study of living cells.

A functional RNA/DNA circuit for one-pot detection of SARS-CoV-2 RNA

A simple method is proposed in this work for the detection of SARS-CoV-2 RNA based on a functional RNA/DNA circuit. By ingeniously integrating the nucleic acid circuit technology and CRISPR/cas12a system, this method can achieve femtomolar detection of the target RNA in one step and successfully distinguish COVID-19 positive cases from clinical samples, proving its great potential for clinical application.

Dual DNAzyme-catalytic assembly of G-quadruplexes for inducing the aggregation of gold nanoparticles and developing a novel antibiotic assay method

By utilizing a target biorecognition reaction to induce the self-assembly of G-quadruplexes and the aggregation of gold nanoparticles (Au NPs), this work develops a novel colorimetric biosensing method for kanamycin (Kana) antibiotic detection. The compact G-quadruplex structure was assembled from its two half-split sequences which were designed in two hairpin substrates of the Mg²⁺-dependent DNAzyme (MNAzyme). Besides hybridizing with the aptamer strand, the MNAzyme sequence was also split into two half fragments to be designed in the two substrates. Upon the aptamer-recognition reaction toward Kana, the MNAzyme strand could be quantitatively released to cause the exposure of the split G-quadruplex-sequences on two hairpin substrate-modified Au NPs and simultaneous release of two half fragments of the MNAzyme-sequence. Thus, the K⁺-assisted self-folding of G-quadruplexes causes the cross-linking of the two Au NPs to realize the Au NP aggregation-based colorimetric signal output (measured at the largest absorption peak near 520 nm). Meanwhile, the self-assembled formation of the second MNAzyme drastically amplified the signal response. Under the optimal conditions, a wide linear range from 0.1 pg mL^-1 to 10 ng mL^-1 and an ultrahigh sensitivity with the detection limit of 76 fg mL^-1 were obtained. The dose-recovery experiments in real samples showed satisfactory results with recoveries from 98.4 to 105.4% and relative errors compared with the ELISA method less than 4.1%. Due to the high selectivity, excellent repeatability and stability, and simple manipulation, this method indicates a promising potential for practical applications. A novel homogeneous biosensing method was developed for the convenient detection of the kanamycin antibiotic. The target biorecognition-induced and dual DNAzyme-catalytic assembly of G-quadruplexes enabled the amplified aggregation of gold nanoparticles for the simple, cheap, stable, and ultrasensitive colorimetric signal transduction of the method.

Structure and function encoding of a bidirectional activatable synergetic DNA machine for speeded and ultrasensitive determination of microRNAs

This work describes the unique design of a bidirectional activatable synergetic DNA machine (BAS-DNA machine) for speeded and ultrasensitive determination of microRNA-21 (miR-21), a well-known biomarker for biomedical research and early diagnosis of lung cancer. The BAS-DNA machine is composed by a pair of track strands (Track 1 and Track 2) encoding with two regions in the opposite direction for miR-21 recognition. Introduction of miR-21 can hybridize either with Track 1 or with Track 2 to activate the BAS-DNA machine with a synergistic effect for speeded amplifying the fluorescence signal. Moreover, compared with common DNA machine with only one switch for exogenous target recognition, the BAS-DNA machine with two switches for miR-21 binding allows the speeded and strong operation of the autonomous strand scission, replication, and displacement on Track 1 and Track 2 simultaneously. This behavior makes the BAS-DNA machine powerful for ultrasensitive, specific, and fast screening of miR-21 even from real biological samples, and the fluorescence signal was found to be linear from 1 pM to 10 nM with a detection limit of 703.6 fM. We envision this BAS-DNA machine with its superior assay performance will provide a new avenue for simple, sensitive, and affordable biomedical assays.

A Versatile Platform for Sensitive and Label-Free Identification of Biomarkers through an Exo-III-Assisted Cascade Signal Amplification Strategy

The development of a versatile and sensitive analytical biomarker detection platform is important for both early diagnosis and treatment of diseases. In the present study, we propose a novel fluorescence-based, ultrasensitive, and label-free biomarker detection platform. This platform relies on a flexible probe design compatible for multiple biomarker identification and Exo-III enzyme-triggered cascade signal amplification. We have validated that this label-free platform exhibits high sensitivity and specificity. Indeed, this platform exhibited brilliant analytical performance in qualifying a carcinoembryonic antigen and small extracellular vesicles (sEVs). It also shows excellent capability in multiplexing mapping of surface proteins of various cancer-derived sEVs. Therefore, we believe that the proposed sensing platform has great potential for clinical diagnosis and anticancer drug development.

Mycobacterium tuberculosis piezoelectric sensor based on AuNPs-mediated enzyme assisted signal amplification

Rapid diagnosis of tuberculosis disease (TB) still remained a pressing need for TB control efforts all over the world. However, the existing detection approaches cannot satisfy demand of rapid detection of clinical Mycobacterium tuberculosis (M. tuberculosis) because of the long detection time and high cost. Herein, we proposed a new M. tuberculosis piezoelectric sensor based on AuNPs-mediated enzyme assisted signal amplification. A hairpin-shaped DNA duplex with a protrusion of the 3' end was designed. In the presence of specific 16 S rDNA fragment of M. tuberculosis, the hairpin probe was opened, which triggered the selective cleavage of hairpin probe by Exonuclease III (Exo III), resulting in the release of uncut DNA probe and target DNA. The released target DNA hybridized with another hairpin-shaped DNA duplex, and a new digestion cycle was started, thus generating large amounts of uncut DNA probes. The uncut DNA was pulled to the electrode surface by the hybridization with capture probe modified on the electrode. Subsequently detection probe labeled AuNPs was hybridized with uncut DNA and entered between the two electrodes. The AuNPs linked to hybridized detection probe were grown in the HAuCl₄ and Nicotinamide adenine dinucleotide (NADH) solution and offered the conductive connection between the gaps of electrode. The changes were monitored by the piezoelectric sensor. The piezoelectric biosensor could achieve a detection of M. tuberculosis (10²-10⁸ CFU mL^-1) within 3 h, the detection limit (LOD) was 30 CFU mL^-1. The methodology could be transformed into different microbial targets, which is suitable for further development of small portable equipment and multifunctional detection.

Multivalent self-assembled nano string lights for tumor-targeted delivery and accelerated biomarker imaging in living cells and in vivo

Multivalent self-assembled nano string lights for tumor-targeted delivery with high efficiency and accelerated biomarker imaging in living cells and in vivo.

Electrochemical sensor propelled by exonuclease III for highly efficient microRNA-155 detection

We constructed an electrochemical sensor, propelled by exonuclease III, for highly efficient microRNA-155 detection. The detection performance of the sensor was excellent, with a detection limit as low as 0.035 fM.

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.

Recent advances in the exonuclease III-assisted target signal amplification strategy for nucleic acid detection

The detection of nucleic acids has become significantly important in molecular diagnostics, gene therapy, mutation analysis, forensic investigations and biomedical development, and so on. In recent years, exonuclease III (Exo III) as an enzyme in the 3'-5' exonuclease family has evolved as a frequently used technique for signal amplification of low level DNA target detection. Different from the traditional target amplification strategies, the Exo III-assisted amplification strategy has been used for target DNA detection through directly amplifying the amounts of signal reagents. The Exo III-assisted amplification strategy has its unique advantages and characters, because the character of non-specific recognition of Exo III can overcome the limitation of a target-to-probe ratio of 1 : 1 in the traditional nucleic acid hybridization assay and acquire higher sensitivity. In this review, we selectively discuss the recent advances in the Exo III-assisted amplification strategy, including the amplification strategy integrated with nanomaterials, biosensors, hairpin probes and other nucleic acid detection methods. We also discuss the strengths and limitations of each strategy and methods to overcome the limitations.

Photoelectrochemical Assay Based on SnO2/BiOBr p-n Heterojunction for Ultrasensitive DNA Detection

Herein, a photoelectrochemical (PEC) assay was designed for a highly sensitive DNA determination relying upon the SnO₂/BiOBr p-n heterojunction as a photoactive material and SiO₂ as a signal quencher. Compared with most traditional heterojunctions, the SnO₂/BiOBr p-n heterostructure not only lessened the recombination of the photogenerated electron-hole pairs but also promoted the light-harvesting in the ultraviolet-visible (UV-vis) region, leading to further enhanced photoelectric conversion efficiency and photocurrent, which demonstrated 12.1-fold and 6.4-fold increments versus those of pure SnO₂ and BiOBr, respectively. Additionally, the limited quantity of target DNA (a fragment of p53 gene) could be transformed into abundant output DNA-SiO₂ by employing the Nt·BstNBI enzyme-assisted signal amplification procedure, leading to a highly improved detection sensitivity of the biosensor. Then, output DNA-SiO₂ hybridized with the capture DNA anchored on the modified electrode surface, remarkably diminishing the PEC signal and thus achieving sensitive DNA determination. The elaborated PEC biosensor demonstrated outstanding performance within the linear range between 0.5 fM and 5 nM and a low limit of detection down to 0.18 fM, paving a new way for fabricating heterojunction with exceptional photoactive performance and demonstrating the enormous potential for detecting multitudinous biomarkers in bioanalysis and clinical therapy.

Isothermal Self-Primer EXPonential Amplification Reaction (SPEXPAR) for Highly Sensitive Detection of Single-Stranded Nucleic Acids and Proteins

Development of versatile sensing methods for sensitive and specific detection of clinically relevant nucleic acids and proteins is of great value for disease monitoring and diagnosis. In this work, we propose a novel isothermal Self-primer EXPonential Amplification Reaction (SPEXPAR) strategy based on a rationally engineered structure-switchable Metastable Hairpin template (MH-template). The MH-template initially keeps inactive with its self-primer overhanging a part of target recognition region to inhibit polymerization. The present targets can specifically compel the MH-template to transform into an "activate" conformation that primes a target-recyclable EXPAR. The method is simple and sensitive, can accurately and facilely detect long-chain single-stranded nucleic acids or proteins without the need of exogenous primer probes, and has a high amplification efficiency theoretically more than 2ⁿ. For a proof-of-concept demonstration, the SPEXPAR method was used to sensitively detect the characteristic sequence of the typical swine fever virus (CSFV) RNA and thrombin, as nucleic acid and protein models, with limits of detection down to 43 aM and 39 fM, respectively, and even the CSFV RNA in attenuated vaccine samples and thrombin in diluted serum samples. The SPEXPAR method may serve as a powerful technique for the biological research of single-stranded nucleic acids and proteins.

DNA Structure-Stabilized Liquid-Liquid Self-Assembled Ordered Au Nanoparticle Interface for Sensitive Detection of MiRNA 155

Au nanoparticles (Au NPs) can be self-assembled in a bottom-up orderly manner at the oil-water interface, which is widely used as SERS platforms, but the stability of the Au NP interface needs to be improved due to shaking or shifting and the Brownian motion. The DNA structure with unique sequence specificity, excellent programmability, and flexible end-group modification capability owns good potential to precisely control the plasmonic structure's distance. In this study, a large area of the SERS substrate is obtained from the DNA structure-stabilized self-assembled ordered Au NPs on the cyclohexane-water interface. Combining with the exonuclease III (exo III)-assisted DNA recycling amplification strategy, we construct a liquid-phase SERS biosensor for efficient detection of microRNA 155 (miRNA 155). Compared with the traditional randomly assembled Au NPs on the two-phase interface, the SERS signal is significantly enhanced and more stable. The detection limit of the SERS biosensor for miRNA 155 reached 1.45 fmol/L, which has a very wide linear range (100 fmol/L-5 nmol/L). This work gives an efficient approach to stabilize the self-assembly Au NPs on the liquid-liquid interface, which can broaden the application of SERS analysis.

Template-free multiple signal amplification for highly sensitive detection of cancer cell-derived exosomes

In this work, we have designed a template-free multiple signal amplification method for the highly sensitive detection of cancer cell-derived exosomes. In this design, DNase I serves as a bridge to link the DNA-based amplification approach and terminal deoxynucleotidyl transferase (TdT)-mediated polymerization reaction. Consequently, a detection limit of 10 particles per μL can be achieved, while a complex nucleic acid sequence design can be avoided. This method also exhibits good performance in a complicated matrix and enables the differentiation of healthy individuals from colorectal cancer (CRC) patients.

Surface-enhanced Raman scattering holography chip for rapid, sensitive and multiplexed detection of human breast cancer-associated MicroRNAs in clinical samples

MicroRNAs (miRNAs) are promising biomarkers for the early diagnosis of breast cancer. Yet, simultaneous achievement of rapid, sensitive and accurate detection of diverse miRNAs in clinical samples is still challenging due to the low abundance of miRNAs and the complex procedures of RNA extraction and separation. Herein, we develop an innovative three-dimensional (3D) surface-enhanced Raman scattering (SERS) holography sensing strategy for rapid, sensitive and multiplexed detection of human breast cancer-associated miRNAs. To establish a proof of concept, nine kinds of human breast cancer-associated miRNAs are isothermally amplified by Exonuclease (Exo) III enzyme, and the products could be spatially separated to corresponding sensing region on silicon SERS substrates. Each region has been modified with corresponding hairpin DNA probes, which are used to identify and quantify the miRNAs. Different DNA probes are labeled with different Raman reporters, which serve as "SERS tags" to incorporate spectroscopic information into computer-generated 3D SERS hologram within ~9 min. We demonstrate that 3D SERS holography chip not only achieves an ultrahigh sensitivity down to ~1 aM but also feature a high correlation with RT-qPCR in the detection of nine miRNAs in 30 clinical serum samples. This work provides a feasible tool to improve the diagnosis of breast cancer.

Nucleic Acid Amplification Techniques in Immunoassay: An Integrated Approach with Hybrid Performance

An immunoassay is mostly employed for the direct detection of food contaminants, and a molecular assay for targeting nucleic acids employs amplification techniques for distinguishing genes. The integration of an immunoassay with nucleic acid amplification techniques inherits the direct and rapid performance of an immunoassay and the ultrasensitive merit of a molecular assay. Enthusiastic attention has been attracted in recent years on the utilization of isothermal amplification techniques in an immunoassay, as well as the employment of a lateral flow immunoassay in a molecular assay. Thus, this Review discussed these kinds of approaches from two categories: immuno-nucleic acid amplification (I-NAA) and nucleic acid amplification-immunoassay (NAA-I). The advantages, drawbacks, and future developments were discussed for a comprehensive understanding.

Fe3O4@polydopamine and Exo III-assisted homogeneous biorecognition reaction for convenient and ultrasensitive detection of kanamycin antibiotic

Herein, we report a Fe3O4@polydopamine (PDA) nanocomposite and exonuclease III (Exo III)-assisted homogeneous fluorescence biosensing method for ultrasensitive detection of kanamycin (Kana) antibiotic. A hairpin DNA containing the Kana-aptamer sequence (HP) was first designed for the highly specific biorecognition of the target analyte. Because of the aptamer biorecognition-induced structural change of HP and the highly effective catalyzed reaction of Exo III, a large amount of fluorophore labels were released from the designed fluorescence DNA probe. During the homogeneous reaction process, the Exo III-assisted dual recycling significantly amplified the fluorescence signal output. Moreover, the excessive probes were easily adsorbed and separated by the Fe3O4@PDA nanocomposite, which decreased the background signal and increased the signal-to-noise ratio. These strategies result in the excellent analytical performance of the method, including a very low detection limit of 0.023 pg mL-1 and a very wide linear range of six orders of magnitude. In addition, this method has convenient operation, excellent selectivity, repeatability and satisfactory reliability, and does not involve the design and utilization of complicated DNA sequences. Thus, it exhibits a promising prospect for practical applications.

A hairpin probe-mediated DNA circuit for the detection of the mecA gene of Staphylococcus aureus based on exonuclease III and DNAzyme-mediated signal amplification

A simple, highly sensitive biosensor for S. aureus detection is becoming increasingly important in human health and safety. In this work, a hairpin probe-mediated DNA circuit for the detection of the mecA gene of S. aureus was reported cascading Exo III-assisted cycling signal amplification and the DNAzyme-mediated cleavage reaction. In the presence of the target mecA gene, the recognition and hybridization between HP1 and mecA can trigger Exo III and DNAzyme-mediated signal amplification and further release numerous ATMND, resulting in an enhanced fluorescence response, which serves as a response signal for the fluorescence detection of mecA gene. This biosensor enables the sensitive and specific detection of the mecA gene, showing a linear response ranging from 1 fM to 1 nM with a detection limit of 0.5 fM. Moreover, this fluorescence assay has been applied for the analysis of clinical samples with satisfactory recovery. Importantly, this universal platform can be further extended for the analysis of other targets by alternating the corresponding recognition unit, which holds much promise in point-of-care testing for bacterial analysis.

Magnetic-Assisted Methylene Blue-Intercalated Amplified dsDNA for Polarity-Switching-Mode Photoelectrochemical Aptasensing

Organic dyes are typically applied as photosensitizers in photoelectrochemical (PEC) cells but have not been reported in polarity-reversal-mode PEC sensors with excellent sensitivity and accuracy. Herein, an elegant and robust PEC biosensor for carcinoembryonic antigen (CEA) has been designed by photocurrent polarity switching of CdTe quantum dots (QDs), which is obtained by embedding methylene blue (MB) into amplified double-stranded DNA (dsDNA) anchored to the superparamagnetic Fe₃O₄@SiO₂. The target-triggered Exo III-assisted cyclic amplification strategy and in situ magnetic enrichment enable the remarkable sensitivity. The extraction of target-analogue single-stranded DNA (output DNA) contributes to high selectivity resulting from the elimination of possible interferences in real samples or matrixes. Particularly, this exclusive polarity-reversal-mode PEC aptasensing can efficiently eliminate the false-positive or false-negative signals, leading to accurate measurements. Moreover, different from the probes and layer-by-layer assembled photoelectric beacons on electrodes in advance, this rational split-type approach is doomed to help the PEC biosensor with additional merits of convenient fabrication, short time consumption, wider linearity, as well as outstanding reproducibility and stability in practical applications. In light of the ability of MB acting as a kind of signal probe in typical electrochemical sensors, certainly, this ingenious design can not only be extended to a wide variety of target monitoring but also provide new ideas for the construction of high-performance electrochemical and PEC biosensors.