Improving the Signal-to-Background Ratio during Catalytic Hairpin Assembly through Both-End-Blocked DNAzyme

Primer Exchange Reaction with Cascade RNA Transcription for Highly Specific Detection of Exosomal miRNA and Liver Cancer Diagnosis

Exosomal microRNAs (miRNAs) serve as dependable and noninvasive biomarkers for early cancer diagnosis. However, the accurate and feasible detection of exosomal miRNAs is often hindered by their low abundance and the requirement of specialized equipment for miRNA detection. In this study, we present a novel approach, termed primer exchange reaction-based fluorescence emission with cascade RNA aptamers transcription (PERFECT) for the highly sensitive detection of exosomal miRNA. The design of this method involves the selective interaction of a DNA probe with the target miRNA, leading to its activation. Once activated, isothermal signal amplification and RNA aptamer transcription are initiated, resulting in an amplified fluorescent signal within 90 min. This method achieves a detection limit of 2.2 fM at 37 °C and 2.7 fM at room temperature (25 °C). We used the PERFECT technology to analyze miR-21 expression levels in cell extracts, cell-derived exosomes, and human plasma-derived exosomes, achieving a diagnostic accuracy of 93.6% in distinguishing hepatocellular carcinoma (HCC) patients. Overall, this study highlights its broad range of detection temperature, simplicity of the detection process, and strong potential for clinical application, rendering it a promising tool for early cancer diagnosis.

Exploration and Application of the Catalytic Superiority of Non-G-Quadruplex Hemin Aptamers

A newly identified hemin aptamer with a non-G-quadruplex structure exhibits stronger peroxidase activity and selectivity than traditional G-quadruplex/hemin DNAzymes, addressing challenges such as weak hemin binding, low catalytic activity, and poor selectivity. In this study, we optimized ion activation conditions, refined reaction parameters, and developed a spontaneous recombination method via aptamer splitting to enhance DNAzyme activity and enable activity regulation. The aptamer demonstrated superior performance in enzyme-free sensing, polymerase-assisted amplification, and CRISPR/Cas12a systems, achieving higher sensitivity and improved colorimetric thresholds compared to G-quadruplexes. We have also developed a comprehensive operational guide for aptamer/hemin DNAzymes, which is poised to revolutionize colorimetric sensor signal generation elements.

Label-free colorimetric detection platform based on catalytic hairpin self-assembly and G-quadruplex/hemin DNAzyme for comprehensive biomarker profiling

The expression level of human apurinic/apyrimidinic endonuclease 1 (APE1) is closely associated with the onset of various diseases, establishing it as a crucial clinical biomarker and a target in anti-cancer efforts. This study accomplished colorimetric and visual detection of APE1 by harnessing its endonuclease activity through catalytic hairpin self-assembly (CHA) and G-quadruplex/hemin DNAzyme. Optimization of the freedom degrees of the G-rich sequence significantly improved the detection performance of the strategy by influencing DNAzyme formation. Additionally, we replaced the signal reporting system with a molecular beacon to develop a fluorescence detection strategy, which served as an extension of the signal amplification system for validation and signal readout. The fluorescent probe method achieved a detection limit of 3.37 × 10-4 U/mL, while the colorimetric method yielded a detection limit of 6.5 × 10-3 U/mL, with a linear range spanning from 0.01 to 0.25 U/mL. Subsequently, the colorimetric approach effectively assessed APE1 activity in biological samples and facilitated the screening of APE1 activity inhibitors. Furthermore, this CHA/G-quadruplex/hemin DNAzyme strategy was adapted for the colorimetric detection of adenosine, showcasing its broad applicability across various biomarkers. The developed colorimetric analytical strategy represents a pivotal biosensing platform for diagnosing and treating diseases.

A colorimetric and fluorescent dual-mode sensor based on bifunctional G-quadruplex-hemin complex for the determination of Pb2

Due to the threat of lead pollution to health, environmental and food safety, developing simple and fast detection methods is highly required. Whereas, traditional single-mode probe suffers from limited application scenario. In this study, a colorimetric and fluorometric dual-mode probe for Pb2+ determination was constructed by using bifunctional G-quadruplex-hemin complex. In this dual-mode probe, enzyme strand and substrate strand of 8-17 DNAzyme are labeled with G-quadruplex-hemin complex and fluorophore, respectively. In the absence of Pb2+, the self-assembly of enzyme strand and substrate strand inhibits intrinsic mimic peroxidase of G-quadruplex-hemin complex by base-pairing, which also quench the fluorescence via in proximity effect. When the DNAzyme is activated by Pb2+, the quenched fluorescence is restored as well as the inherent peroxidase mimetic activity, leading to dual signal output. Under optimal conditions, this dual-mode probe exhibit a good linear relationship between logarithm of Pb2+ concentration and signal difference within the range from 1.5 nM to 20 nM and 0.5 nM to 10 nM for colorimetric and fluorescence mode, respectively. The detection limits for the corresponding mode were estimated to be 1.29 nM and 0.16 nM, respectively. This dual-mode probe also successfully applied for the spiked river water assay with satisfactory recovery in the range of 93.2 %-115.3 %. This work paves a new way for DNAzyme based dual-mode probe construction.

Rapid and portable bunyavirus SFTSV RNA testing utilizing catalytic hairpin assembly coupled with lateral flow immunoassay

Severe fever with thrombocytopenia syndrome (SFTS) is a prevalent, life-threatening, emergent infectious disease. Currently, reverse transcription-polymerase chain reaction is the gold standard for diagnosing SFTS virus (SFTSV) infection, which requires sophisticated equipment and professional personnel that are frequently unavailable in most SFTS endemic rural areas. Here, we reported a simple, rapid nucleic acid amplification system that combined the catalytic hairpin assembly (CHA) with a lateral flow immunoassay (LFIA) strip-based detection method for SFTSV detection. The detection of SFTSV RNA could be realized by generation of H1-H2 hybrid duplexes labeled with biotin and digoxin, which subsequently added to the LFIA test strips containing streptavidin conjugated with Alexa Fluor 647 as well as anti-digoxin antibodies. Our CHA-based LFIA assay offered high amplification efficiency and specificity with a detection limit of 1 aM. Crucially, this method enabled stable detection of 500 copies/mL of SFTSV within 30 min using clinical serum samples. Therefore, our CHA-based LFIA approach provided a potential useful tool to facilitate early and precise diagnosis of SFTS patients in poorly resourced SFTS endemic areas.IMPORTANCESevere fever with thrombocytopenia syndrome (SFTS) is an emerging and potentially fatal infectious disease prevalent in China. Here we report a simple, rapid nucleic acid amplification system, the catalytic hairpin assembly (CHA) in conjunction with a lateral flow immunoassay (LFIA) strip-based detection method for SFTS virus detection, which demonstrated high amplification efficiency and specificity with limit of detection of 1 aM. Most importantly, we also validate our CHA-based LFIA assay using the clinical serum samples, which was fully compatible with reverse transcription-PCR results. Therefore, our strategy provides a potential useful tool to facilitate early and precise diagnosis of SFTS patients especially in poorly resourced SFTS endemic areas.

An overview of biochemical technologies for the cancer biomarker miR-21 detection

In recent years, the incidence of cancer has continuously increased, in which various miRNAs have been proposed as biomarkers for the early screening of cancer patients. As a consequence, the development of accurate methods for miRNA quantification has become a major research challenge worldwide. As one of the first discovered oncogenic miRNAs, microRNA-21 (miR-21) has been highlighted for its critical role in cancers. This review describes the main techniques currently available for miR-21 detection, compares the differences of the methods and the amplification strategies, and provides an overview of the state of knowledge in the field.

Aggregation-Induced Emission Effect within Peroxyoxalate-Loaded Mesoporous Silica Nanoparticles for Efficient Harvest of Chemiluminescence Energy in Aqueous Solutions

Aggregation-induced emission (AIE) molecules that can avoid the aggregation-caused quenching (ACQ) effect and break the concentration limit have been widely used for biosensing. Similar to fluorescence dyes, AIE molecules can be chemiexcited simply by a peroxyoxalate-based chemiluminescence (CL) reaction, but the hydrolysis of peroxyoxalate is often a problem in an aqueous solution. Herein, we report an AIE effect within peroxyoxalate-loaded silica nanoparticles (PMSNs) for an efficient harvest of CL energy as well as alleviation of bis(2,4,5-trichloro-6-carbopentoxyphenyl) oxalate (CPPO) hydrolysis. Peroxyoxalate (i.e., CPPO) and AIE molecules (i.e., 1,2-benzothiazol-2-triphenylamino acrylonitrile, BTPA) were loaded together within the mesoporous silica nanoparticles (MSNs) to synthesize the BTPA-PMSN nanocomposite. The BTPA-PMSNs not only allowed CPPO to be dispersed well in an aqueous solution but also avoided the hydrolysis of CPPO. Meanwhile, the proximity between BTPA and CPPO molecules in the mesopores of MSNs facilitated the BTPA aggregate to harvest the energy from CL intermediates. Hence, the CL system of BTPA-PMSNs can work efficiently in aqueous solutions at a physiological pH. The CL quantum yield of the BTPA-PMSN system was measured to be 9.91 × 10^-5, about 20 000-fold higher than that obtained in the rhodamine B (RhB, a typical ACQ dye)-PMSN system. Using BTPA-PMSNs for H₂O₂ sensing, a limit of detection (LOD) as low as 5 nM can be achieved, 1000-fold lower than that achieved in the RhB-PMSNs system. Due to the feasibility of working at a physiological pH, this CL system is also quite suitable for the detection of oxidase substrates such as glucose and cholesterol. This BTPA-PMSN CL system with the merits of high CL quantum yield at a physiological pH is appealing for biosensing.

Multiply-amplified strategy for the ultrasensitive detection of kanamycin via aptamer-triggered three-dimensional G-quadruplex/Ni-Fe layered double oxide frame networks

In this work, a multiply-amplified peroxidase-like colorimetric strategy was proposed for the high-specific recognition and ultrasensitive detection of kanamycin (Kana). Based on two Kana-aptamer triggered sequential reactions, G-quadruplex (G4) and DNA (hairpins) modified Ni-Fe layered double oxides (LDOs) could be obtained simultaneously. Later, a three-dimensional G4/LDO frame networks, as a novel DNAzyme, with enhanced peroxidase-like catalytic activity was assembled through electrostatic interaction. This DNAzyme catalyzed 3,3',5,5'-tetramethylbenzidine oxidation for the colorimetric detection of Kana. The enhancement principle was discussed and the charge transfer process during the catalytic reaction was investigated. Under the optimal experiment conditions, the proposed method exhibited high sensitivity, where the linear range is from 10 fM to 10 nM (r² = 0.992), and the limit of detection is 3 fM (S/N = 3). The practicability of this assay was demonstrated by successfully application of residual Kana detection in genuine milk and urine samples.

A Colorimetric Strategy Based on Aptamer-Catalyzed Hairpin Assembly for the On-Site Detection of Salmonella typhimurium in Milk

Salmonella typhimurium (S. typhimurium) is a foodborne pathogen that has caused numerous outbreaks worldwide, necessitating the development of on-site strategy to prevent early contamination. Here, we set up an enzyme-free strategy for aptamer-catalyzed hairpin assembly in which salt-induced aggregation of unmodified gold nanoparticles (AuNPs) served as a colorimetric signal output, allowing on-site detection of S. typhimurium in milk. The aptamer-functionalized magnetic beads were used as a vehicle of specifically enriching target bacteria which conjugated with target aptamer to trigger the “Y” shape catalytic hairpin assembly (Y-CHA) circuit. Due to the hairpins desorbing from the surface of AuNPs to the formation of a large amount of double-stranded DNA (dsDNA), AuNPs turned from dispersion to aggregation in the presence of S. typhimurium, resulting in a change of the colorimetric signal from red to blue-gray. The signal output showed a linear relationship for S. typhimurium over a concentration range of 10² to 10⁶ CFU/mL, with a sensitivity of 2.4 × 10² CFU/mL under optimal conditions. The visual protocol has excellent selectivity even in the presence of other competitive bacteria and has been validated in real milk samples with a sensitivity of 2.8 × 10³ CFU/mL.

A Deoxyribozyme-Initiated Self-Catalytic DNA Machine for Amplified Live-Cell Imaging of MicroRNA

Functional DNA nanostructures have been widely used in various bioassay fields. Yet, the programmable assembly of functional DNA nanostructures in living cells still represents a challenging goal for guaranteeing the sensitive and specific biosensing utility. In this work, we report a self-catalytic DNA assembly (SDA) machine by using a feedback deoxyribozyme (DNAzyme)-amplified branched DNA assembly. This SDA system consists of catalytic self-assembly (CSA) and DNAzyme amplification modules for recognizing and amplifying the target analyte. The analyte initiates the CSA reaction, leading to the formation of Y-shaped DNA that carries two RNA-cleaving DNAzymes. One DNAzyme can then successively cleave the corresponding substrate and generate numerous additional inputs to activate new CSA reactions, thus realizing a self-catalytic amplification reaction. Simultaneously, the other DNAzyme is assembled as a versatile signal transducer for cleaving the fluorophore/quencher-modified substrate, leading to the generation of an amplified fluorescence readout. By incorporating a flexible auxiliary sensing module, the SDA system can be converted into a universal sensing platform for detecting cancerous biomarkers, e.g., a well-known oncogene microRNA-21 (miR-21). Moreover, the SDA system realized the precise intracellular miR-21 imaging in living cells, which is attributed to the reciprocal amplification property between CSA reactions and DNAzyme biocatalysis. This compact SDA amplifier machine provides a universal and facile toolbox for the highly efficient identification of cancerous biomarkers and thus holds great potential for early cancer diagnosis.

Algorithm-Assisted Detection and Imaging of microRNAs in Living Cancer Cells via the Disassembly of Plasmonic Core-Satellite Probes Coupled with Strand Displacement Amplification

Acute detection and high-resolution imaging of microRNAs (miRNAs) in living cancer cells have attracted great attention in clinical diagnosis and therapy. However, current methods suffer from low detection sensitivity or heavy dependence on expensive and sophisticated spectrometers. Herein, a novel algorithm-assisted system of detecting and imaging miRNAs in living cancer cells was developed via the disassembly of plasmonic core-satellite probes coupled with strand displacement amplification (SDA). The target miRNAs in the system could trigger the disassembly of plasmonic core-satellite probes, leading to the color change in the scattering light of the probes, which could be captured by dark-field microscopy (DFM). The concentration of the target miRNAs was obtained by analyzing the dark-field image based on the proposed algorithm with a detection limit of 2 pM for miRNA-21. Thus, the performance in terms of simplicity and sensitivity of the system compared with one of the conventional spectrophotometers was well presented, which could inspire more clinical applications of inexpensive, intelligent, and rapid screening of cancer cells. The application software based on the proposed algorithm running on the Android platform was also developed, demonstrating the potential of remote diagnosis.

DNAzyme-Metal-Organic Framework Two-Photon Nanoprobe for In situ Monitoring of Apoptosis-Associated Zn2+ in Living Cells and Tissues

Monitoring Zn²⁺ in living cells is critical for fully elucidating the biological process of apoptosis. However, the quantitative intracellular sensing of Zn²⁺ using DNAzyme remains challenging because of issues related to penetration of the signal through tissue, targeted cellular uptake and activation, and susceptibility toward enzymatic degradation. In this study, we developed a novel phosphate ion-activated DNAzyme-metal-organic frameworks (MOFs) nanoprobe for two-photon imaging of Zn²⁺ in living cells and tissues. The design of this nanoprobe involved the loading of a Zn²⁺-specific, RNA-cleaving DNAzyme onto the MOFs through strong coordination between the phosphonate O atoms of the DNAzyme backbone and Zr atoms in the MOFs. This coordination restrained the extracellular activity of DNAzyme; however, after cell entry, the DNAzyme was released from the MOFs through a competitive binding by the phosphate ions present at a high intracellular concentration. Following their release, the two-photon (TP) fluorophore-labeled substrate strands of DNAzyme were cleaved with the aid of Zn²⁺, which resulted in a strong fluorescence signal. The incorporation of a TP fluorophore into the nanoprobe facilitated near-infrared excitation, which allowed the highly sensitive and specific imaging of Zn²⁺ in living cells and tissues at greater depths than possible previously. The TP-DNAzyme-MOFs nanoprobe achieved a low detection limit of 3.53 nM, extraordinary selectivity toward Zn²⁺, and a tissue signal penetration of 120 μm. More importantly, this nanoprobe was successfully used to monitor cell apoptosis, and this application of the DNAzyme-MOFs probe holds great potential for future use in biological studies and medical diagnostics.

Suppressing the background activity of hemin for boosting the sensitivity of DNAzyme-based biosensors by SYBR Green I

Peroxidase-like DNAzymes have been extensively used to replace horseradish peroxidase (HRP) for developing biosensors for signal amplification. However, the background activity from the cofactor (i.e., free hemin) has limited the sensitivity of such sensors. Herein, we aim to find an inhibitor for hemin to suppress the background signal, and a classic split DNAzyme-based sensor was used to detect a complementary DNA oligonucleotide. After screening a series of dyes, SYBR Green I (SG, one of the DNA stanning dyes) was selected for suppressing the background. Simply by adding 0.84 μM SG, the background from 50 nM hemin was suppressed over 30-fold. The suppression was caused by the interaction between SG and hemin. In the presence of the target DNA, the formed duplex region and G-quadruplex structure can better bind SG and hemin respectively, thus preventing the interaction between them and showing a high activity of the DNAzyme. The optimized sensor showed a detection limit of 3.8 pM for the target DNA (p53 gene). In addition, the backgrounds from chemiluminescence, colorimetric and fluorescence sensing modes can all be reduced by adding SG to the split DNAzyme system. The suppression of the background of peroxidase DNAzymes is a critical step towards practical use of related biosensors.

One-Step Synthesis of Methylene Blue-Encapsulated Zeolitic Imidazolate Framework for Dual-Signal Fluorescent and Homogeneous Electrochemical Biosensing

In vitro diagnosis requires target biomarkers to be reliably detected at an ultralow level. A dual-signal strategy permits self-calibration to overcome the interferences of experimental and environmental factors, and thus is regarded as a promising approach. However, currently reported works mainly concentrated on the same forms of energy of output signals. Herein, we propose a one-step strategy for synthesis of methylene blue-encapsulated zeolitic imidazolate framework-90 (MB@ZIF-90) with high loading, unique dual-signal property, exceptional recognition capability, and good stability, and we further pioneer MB@ZIF-90 as a dual-signal biosensor for label-free, enzyme-free, and ultrasensitive detection of adenosine triphosphate (ATP) by integration of fluorescence and homogeneous electrochemical techniques. The recognition of MB@ZIF-90 by target ATP spurs the decomposition of ZIF-90, subsequently permitting MB to be released into a supernatant. As compared to the case where ATP does not exist, obviously increased intensities in fluorescence and differential pulse voltammetry current are observed and both signals are directly proportional to ATP concentrations. Thus, the MB@ZIF-90-based biosensor achieved dual-signal detection of ATP in an ultrasensitive manner and displayed a more reliable diagnosis result than previously reported ATP biosensors. This dual-signal strategy provides a new opportunity to develop high-performance biosensors for in vitro diagnosis and demonstrates great potential for future applications in bioinformatics and clinical medicine.

A Novel Cell-Assisted Enhanced Chemiluminescence Strategy for Rapid and Label-Free Detection of Tumor Cells in Whole Blood

In this study, an interesting phenomenon was found where cells (including tumor and normal cells) managed to significantly enhance chemiluminescence (CL) signals. The possible reaction mechanism may be that cells can be severely damaged by CL substrates, and the released contents, possibly proteins (such as cytochrome c), can remarkably magnify CL owing to the increased production of singlet oxygen. More importantly, based on the above phenomena, a novel cell-assisted enhanced CL strategy was proposed for the rapid and label-free detection of tumor cells. The complexes of aptamer sgc8c and streptavidin-modified magnetic beads were employed to recognize and isolate target tumor cells from whole blood. The enhanced CL intensity, which was triggered directly by the captured cells, was measured. The proposed strategy exhibited a good detection performance with a linear range from 200 to 10,000 cells/mL. The analysis can be finished in ∼30 min, and the limit of detection was down to 100 cells/mL. The recoveries and relative standard deviations were 97.81-102.71% and 3.46-12.71%, respectively. Moreover, the established method can successfully distinguish the leukemia patients from healthy people. Therefore, it provides a novel, rapid, and simple method for the determination of tumor cells, which can be used in further practice.

DNA circuits driven by conformational changes in DNAzyme recognition arms

DNA computing plays an important role in nanotechnology due to the unique programmability and parallelism of DNA molecules. As an important tool to realize DNA computation, various logic computing devices have great application potential. The application of DNAzyme makes the achievements in the field of logical computing more diverse. In order to improve the efficiency of the logical units run by DNAzyme, we proposed a strategy to regulate the DNA circuit by the conformational change of the E6-type DNAzyme recognition arms driven by Mg2+. This strategy changes the single mode of DNAzyme signal transmission, extends the functions of E6-type DNAzyme, and saves the time of signal transmission in the molecular scale. To verify the feasibility of this strategy, first, we constructed DNA logic gates (YES, OR, and AND). Second, we cascade different logic gates (YES-YES, YES-AND) to prove the scalability. Finally, a self-catalytic DNA circuit is established. Through the experimental results, we verified that this DNAzyme regulation strategy relatively reduces the cost of logic circuits to some extent and significantly increases the reaction rate, and can also be used to indicate the range of Mg2+ concentrations. This research strategy provides new thinking for logical computing and explores new directions for detection and biosensors.

Applications of Catalytic Hairpin Assembly Reaction in Biosensing

Nucleic acids are considered as perfect programmable materials for cascade signal amplification and not merely as genetic information carriers. Among them, catalytic hairpin assembly (CHA), an enzyme-free, high-efficiency, and isothermal amplification method, is a typical example. A typical CHA reaction is initiated by single-stranded analytes, and substrate hairpins are successively opened, resulting in thermodynamically stable duplexes. CHA circuits, which were first proposed in 2008, present dozens of systems today. Through in-depth research on mechanisms, the CHA circuits have been continuously enriched with diverse reaction systems and improved analytical performance. After a short time, the CHA reaction can realize exponential amplification under isothermal conditions. Under certain conditions, the CHA reaction can even achieve 600 000-fold signal amplification. Owing to its promising versatility, CHA is able to be applied for analysis of various markers in vitro and in living cells. Also, CHA is integrated with nanomaterials and other molecular biotechnologies to produce diverse readouts. Herein, the varied CHA mechanisms, hairpin designs, and reaction conditions are introduced in detail. Additionally, biosensors based on CHA are presented. Finally, challenges and the outlook of CHA development are considered.

Application of hairpin DNA-based biosensors with various signal amplification strategies in clinical diagnosis

Biosensors have been commonly used in biomedical diagnostic tools in recent years, because of a wide range of application, such as point-of-care monitoring of treatment and disease progression, drug discovery, commonly use food control, environmental monitoring and biomedical research. Additionally, development of DNA biosensors has been increased enormously over the past few years as confirmed by the large number of scientific publications in this field. A wide range of techniques can be used for the development of DNA biosensors, such as DNA nano-machines and various signal amplification strategies. This article selectively reviews the recent advances in DNA base biosensors with various signal amplification strategies for detection of cancer DNA and microRNA, infectious microorganisms, and toxic metal ions.

Construction of a Cytosine-Adjusted Electrochemiluminescence Resonance Energy Transfer System for MicroRNA Detection

The cytosines in cluster-nucleation sequences play a vital role in the formation of silver nanoclusters (Ag NCs). Here, an innovative electrochemiluminescence (ECL) resonance energy transfer (RET) sensing system was developed using CdS quantum dots (QDs) as ECL donor and Ag NCs as ECL acceptor. Modulation of the number of cytosines in the cluster-nucleation sequences allowed tuning of Ag NCs absorption bands to match with the ECL emission spectrum of CdS QDs, yielding effective ECL-RET. The sensitivity of detection was improved by dual-target recycling amplification based on duplex-specific nuclease (DSN) and catalytic hairpin assembly. In the presence of target microRNA-21 (miRNA-21), DSN selectively cleaved the complementary DNA section (S1), resulting in the release of the transduction section (S2) and the reuse of miRNA-21 in the next recycling amplification. Interaction of the stem-loop structure of the DNA1 segment (H1) on CdS QDs-modified electrode with S2 led to the opening of the hairpin structure of H1 and the formation of H1:S2 duplex. Then, hairpin DNA2 encapsulated Ag NCs hybridized with the remaining single-stranded DNA segment of H1, and the S2 strand was replaced. Finally, the dissociated S2 participated in subsequent reaction cycles, introducing Ag NCs to the electrode surface and leading to ECL signal quenching of the CdS QDs. The proposed sensor showed excellent performance in detecting miRNA-21 at a wide linear range from 1 fM to 100 pM. The practical application ability of the strategy was tested in HeLa cells with acceptable results, suggesting that the detection platform is a promising approach for disease diagnosis and molecular biology research.

Turn-off colorimetric sensor for sequence-specific recognition of single-stranded DNA based upon Y-shaped DNA structure

A novel turn-off colorimetric sensor for sequence-specific recognition of single-stranded DNA (ssDNA) was established by combining Y-shaped DNA duplex and G-quadruplex-hemin DNAzyme. A G-rich single-stranded DNA (Oligo-1) displays peroxidase mimicking catalytic activity due to the specific binding with hemin in the presence of K+, which was able to catalyze the oxidation of colorless 2,2'-azinobis(3-ethylbenzothiazoline)-6-sulfonic acid (ABTS2-) by H2O2 to generate green ABTS•- radical for colorimetric assay. Oligonucleotide 2 (Oligo-2) was partly complementary with Oligo-1 and the target DNA. Upon addition of target DNA, Oligo-1, Oligo-2 and target DNA can hybridize with each other to form Y-shaped DNA duplex. The DNAzyme sequence of Oligo-1 was partly caged into Y-shaped DNA duplex, resulting in the inactivation of the DNAzyme and a sharp decrease of the absorbance of the oxidation product of ABTS2-. Under the optimum condition, the absorbance decreased linearly with the concentration of target DNA over the range of 1.0-250 nM and the detection limit was 0.95 nM (3σ/slope) Moreover, satisfied result was obtained for the discrimination of single-base or two-base mismatched DNA.