Enzyme-free colorimetric detection of DNA by using gold nanoparticles and hybridization chain reaction amplification

Construction of an enzyme-free concatenated DNA circuit for signal amplification and intracellular imaging

A rationally and modularly engineered two-layered CHA–HCR circuit was constructed for amplified biosensing and bioimaging with high performance.

Nucleic acid circuits have shown promising potential for amplified detection of biomarkers with interest in biologically important engineering applications. In this work, by properly integrating two signal amplification approaches, catalytic hairpin assembly (CHA) and hybridization chain reaction (HCR), a concatenated CHA–HCR system was established as an isothermal enzyme-free amplification strategy for highly sensitive and selective nucleic acid assay. The target catalyzes the self-assembly of CHA hairpin substrates into dsDNA products, where the split segments of HCR trigger are successively connected to drive the subsequent autonomous cross-opening of HCR hairpins, leading to the construction of HCR tandem copolymeric dsDNA nanowires. The resulting HCR copolymer brings a fluorophore donor/acceptor pair into close proximity that allows an efficient generation of FRET readout signal. Moreover, the optimized CHA–HCR circuit, upon the incorporation of an auxiliary sensing module, can be converted into a universal sensing platform for detecting cancerous biomarkers (e.g., a well-known oncogene miR-21) through a convenient easy-to-integrate procedure. The concatenated CHA–HCR amplifier enables accurate intracellular miRNA imaging in living cells, which is especially suitable for in situ amplified detection of lowly expressed endogenous analytes. The inherent synergistically accelerated recognition and hybridization features of CHA–HCR circuit contribute to the amplified detection of endogenous RNAs in living cells. The flexible and programmable nature of the homogeneous CHA–HCR system provides a versatile and robust toolbox for a wide range of research fields, such as in vivo bioimaging, clinical diagnosis and environmental monitoring.

Plasmonic molecular assays: Recent advances and applications for mobile health

Plasmonics-based biosensing assays have been extensively employed for biomedical applications. Significant advancements in use of plasmonic assays for the construction of point-of-care (POC) diagnostic methods have been made to provide effective and urgent health care of patients, especially in resourcelimited settings. This rapidly progressive research area, centered on the unique surface plasmon resonance (SPR) properties of metallic nanostructures with exceptional absorption and scattering abilities, has greatly facilitated the development of cost-effective, sensitive, and rapid strategies for disease diagnostics and improving patient healthcare in both developed and developing worlds. This review highlights the recent advances and applications of plasmonic technologies for highly sensitive protein and nucleic acid biomarker detection. In particular, we focus on the implementation and penetration of various plasmonic technologies in conventional molecular diagnostic assays, and discuss how such modification has resulted in simpler, faster, and more sensitive alternatives that are suited for point-of-use. Finally, integration of plasmonic molecular assays with various portable POC platforms for mobile health applications are highlighted.

Cross-linking gold nanoparticles aggregation method based on localised surface plasmon resonance for quantitative detection of miR-155

MiR-155 plays a critical role in the formation of cancers and other diseases. In this study, the authors aimed to design and fabricate a biosensor based on cross-linking gold nanoparticles (AuNPs) aggregation for the detection and quantification of miR-155. Also, they intended to compare this method with SYBR Green real-time polymerase chain reaction (PCR). Primers for real-time PCR, and two thiolated capture probes for biosensor, complementary with miR-155, were designed. Citrate capped AuNPs (18.7 ± 3.6 nm) were synthesised and thiolated capture probes immobilised to AuNPs. The various concentrations of synthetic miR-155 were measured by this biosensor and real-time PCR method. Colorimetric changes were studied, and the calibration curves were plotted. Results showed the detection limit of 10 nM for the fabricated biosensor and real-time PCR. Also, eye detection using colour showed the weaker detection limit (1 µM), for this biosensor. MiR-133b as the non-complementary target could not cause a change in both colour and UV-visible spectrum. The increase in hydrodynamic diameter and negative zeta potential of AuNPs after the addition of probes verified the biosensor accurately fabricated. This fabricated biosensor could detect miR-155 simpler and faster than previous methods.

Chemical and Biological Sensing Using Hybridization Chain Reaction

Since the advent of its theoretical discovery more than 30 years ago, DNA nanotechnology has been used in a plethora of diverse applications in both the fundamental and applied sciences. The recent prominence of DNA-based technologies in the scientific community is largely due to the programmable features stored in its nucleobase composition and sequence, which allow it to assemble into highly advanced structures. DNA nanoassemblies are also highly controllable due to the precision of natural and artificial base-pairing, which can be manipulated by pH, temperature, metal ions, and solvent types. This programmability and molecular-level control have allowed scientists to create and utilize DNA nanostructures in one, two, and three dimensions (1D, 2D, and 3D). Initially, these 2D and 3D DNA lattices and shapes attracted a broad scientific audience because they are fundamentally captivating and structurally elegant; however, transforming these conceptual architectural blueprints into functional materials is essential for further advancements in the DNA nanotechnology field. Herein, the chemical and biological sensing applications of a 1D DNA self-assembly process known as hybridization chain reaction (HCR) are reviewed. HCR is a one-dimensional (1D) double stranded (ds) DNA assembly process initiated only in the presence of a specific short ssDNA (initiator) and two kinetically trapped DNA hairpin structures. HCR is considered an enzyme-free isothermal amplification process, which shows substantial promise and offers a wide range of applications for in situ chemical and biological sensing. Due to its modular nature, HCR can be programmed to activate only in the presence of highly specific biological and/or chemical stimuli. HCR can also be combined with different types of molecular reporters and detection approaches for various analytical readouts. While the long dsDNA HCR product may not be as structurally attractive as the 2D and 3D DNA networks, HCR is highly instrumental for applied biological, chemical, and environmental sciences, and has therefore been studied to foster a variety of objectives. In this review, we have focused on nucleic acid, protein, metabolite, and heavy metal ion detection using this 1D DNA nanotechnology via fluorescence, electrochemical, and nanoparticle-based methodologies.

A colorimetric method for the sequence-specific recognition of double-stranded DNA on the surface of a silver-coated glass slide

In this study, a colorimetric method for sequence-specific recognition of double-stranded DNA (dsDNA) was established on the surface of a silver-coated glass slide. Oligo-1 was assembled on the surface of a silver-coated glass slide through an Ag–S bond, and Oligo-2 as reporter was used to bind with streptavidin-horseradish peroxidase (SA–HRP). They could bind with target dsDNA that was composed of Oligo-3 and Oligo-4 on the surface of a silver-coated glass slide through triplex formation. The bound HRP could be moved into the solution by DNase I and catalyze the oxidation of 3,3′,5,5′-tetramethylbenzidine (TMB). Therefore, the concentration of target dsDNA could be determined with the colour change of TMB. Under the optimum conditions, the absorbance was proportional to the concentration of target dsDNA over the range of 100 pmol/L to 2.0 nmol/L, with a detection limit of 13 pmol/L. In addition, this method showed good sequence selectivity, enabling it to be further developed for the detection of other polymerase chain reaction (PCR) products.

Exploration of Nanoparticle-Mediated Photothermal Effect of TMB-H2O2 Colorimetric System and Its Application in a Visual Quantitative Photothermal Immunoassay

The exploration of new physical and chemical properties of materials and their innovative application in different fields are of great importance to advance analytical chemistry, material science, and other important fields. Herein, we, for the first time, discovered the photothermal effect of an iron oxide nanoparticles (NPs)-mediated TMB (3,3',5,5'-tetramethylbenzidine)-H2O2 colorimetric system, and applied it toward the development of a new NP-mediated photothermal immunoassay platform for visual quantitative biomolecule detection using a thermometer as the signal reader. Using a sandwich-type proof-of-concept immunoassay, we found that the charge transfer complex of the iron oxide NPs-mediated one-electron oxidation product of TMB (oxidized TMB) exhibited not only color changes, but also a strong near-infrared (NIR) laser-driven photothermal effect. Hence, oxidized TMB was explored as a new sensitive photothermal probe to convert the immunoassay signal into heat through the near-infrared laser-driven photothermal effect, enabling simple photothermal immunoassay using a thermometer. Based on the new iron oxide NPs-mediated TMB-H2O2 photothermal immunoassay platform, prostate-specific antigen (PSA) as a model biomarker can be detected at a concentration as low as 1.0 ng·mL-1 in normal human serum. The discovered photothermal effect of the colorimetric system and the developed new photothermal immunoassay platform open up a new horizon for affordable detection of disease biomarkers and have great potential for other important material and biomedical applications of interest.

Highly sensitive and visual detection of guanosine 3'-diphosphate-5'-di(tri)phosphate (ppGpp) in bacteria based on copper ions-mediated 4-mercaptobenzoic acid modified gold nanoparticles

Guanosine 3'-diphosphate-5'-di(tri)phosphate (ppGpp) plays a crucial role in the gene expression, metabolism, growth, and other significant processes of microorganisms. In this work, a facile sensitive and visual strategy for the detection of ppGpp has been established by developing a colorimetric probe of copper ions (Cu²⁺)-mediated 4-mercaptobenzoic acid (4-MBA) modified gold nanoparticles (AuNPs). The sensing process was characterized by transmission electron microscopy (TEM), zeta potential, dynamic light scattering (DLS) and UV-vis spectroscopy. The strategy not only achieves desirable performance over a wide concentration range (0.05-10 μM), but also exhibits excellent selectivity over other nucleotides and biomolecules. In addition, the results could be visualized by the naked eye. We have demonstrated the determination of ppGpp in Bacillus subtilis lysate samples.

Localized surface plasmon resonance based biosensing

INTRODUCTION

Bioanalytical sensing based on the principle of localized surface plasmon resonance experiences is currently an extremely rapid development. Novel sensors with new kinds of plasmonic transducers and innovative concepts for the signal development as well as read-out principles were identified. This review will give an overview of the development of this field. Areas covered: The focus is primarily on types of transducers by preparation or dimension, factors for optimal sensing concepts and the critical view of the usability of these devices as innovative sensors for bioanalytical applications. Expert commentary: Plasmonic sensor devices offer a high potential for future biosensing given that limiting factors such as long-time stability of the transducers, the required high sensitivity and the cost-efficient production are addressed. For higher sensitivity, the design of the sensor in shape and material has to be combined with optimal enhancement strategies. Plasmonic nanoparticles from bottom-up synthesis with a post-synthetic processing show a high potential for cost-efficient sensor production. Regarding the measurement principle, LSPRi offers a large potential for multiplex sensors and can provide a high-throughput as well as highly paralleled sensing. The main trends are expected towards optimal LSPR concepts which represent cost-efficient and robust point-of-care solutions, and the use of multiplexed devices for clinical applications.

Optical nano-biosensing interface via nucleic acid amplification strategy: construction and application

Modern optical detection technology plays a critical role in current clinical detection due to its high sensitivity and accuracy. However, higher requirements such as extremely high detection sensitivity have been put forward due to the clinical needs for the early finding and diagnosing of malignant tumors which are significant for tumor therapy. The technology of isothermal amplification with nucleic acids opens up avenues for meeting this requirement. Recent reports have shown that a nucleic acid amplification-assisted modern optical sensing interface has achieved satisfactory sensitivity and accuracy, high speed and specificity. Compared with isothermal amplification technology designed to work completely in a solution system, solid biosensing interfaces demonstrated better performances in stability and sensitivity due to their ease of separation from the reaction mixture and the better signal transduction on these optical nano-biosensing interfaces. Also the flexibility and designability during the construction of these nano-biosensing interfaces provided a promising research topic for the ultrasensitive detection of cancer diseases. In this review, we describe the construction of the burgeoning number of optical nano-biosensing interfaces assisted by a nucleic acid amplification strategy, and provide insightful views on: (1) approaches to the smart fabrication of an optical nano-biosensing interface, (2) biosensing mechanisms via the nucleic acid amplification method, (3) the newest strategies and future perspectives.

Comparison of Different Strategies for the Development of Highly Sensitive Electrochemical Nucleic Acid Biosensors Using Neither Nanomaterials nor Nucleic Acid Amplification

Currently, electrochemical nucleic acid-based biosensing methodologies involving hybridization assays, specific recognition of RNA/DNA and RNA/RNA duplexes, and amplification systems provide an attractive alternative to conventional quantification strategies for the routine determination of relevant nucleic acids at different settings. A particularly relevant objective in the development of such nucleic acid biosensors is the design of as many as possible affordable, quick, and simple methods while keeping the required sensitivity. With this aim in mind, this work reports, for the first time, a thorough comparison between 11 methodologies that involve different assay formats and labeling strategies for targeting the same DNA. The assayed approaches use conventional sandwich and competitive hybridization assays, direct hybridization coupled to bioreceptors with affinity for RNA/DNA duplexes, multienzyme labeling bioreagents, and DNA concatamers. All of them have been implemented on the surface of magnetic beads (MBs) and involve amperometric transduction at screen-printed carbon electrodes (SPCEs). The influence of the formed duplex length and of the labeling strategy have also been evaluated. Results demonstrate that these strategies can provide very sensitive methods without the need for using nanomaterials or polymerase chain reaction (PCR). In addition, the sensitivity can be tailored within several orders of magnitude simply by varying the bioassay format, hybrid length or labeling strategy. This comparative study allowed us to conclude that the use of strategies involving longer hybrids, the use of antibodies with specificity for RNA/DNA heteroduplexes and labeling with bacterial antibody binding proteins conjugated with multiple enzyme molecules, provides the best sensitivity.

Rapid detection of staphylococcal enterotoxin B in milk samples based on fluorescence hybridization chain reaction amplification

A rapid, simple, and sensitive method has been developed to detect staphylococcal enterotoxin B (SEB). To establish the hybridization chain reaction-based aptasensor, we described the new probes of two hairpins (H1 and H2), which were first designed based on the partial complementary sequence of the SEB aptamer (cDNA). The H1 labeled with a fluorophore and a quencher can act as a molecular fluorescence “switch”. Hence, in the presence of SEB, the aptamer binds SEB, while the unbound cDNA triggers HCR to carry out the cyclic hybridization of H1 and H2 so as to turn “ON” the fluorescence through forming long nicked DNA. By using this new strategy, SEB can be sensitively detected within the range of 3.13 ng mL⁻¹ to 100 ng mL⁻¹ with a detection limit of 0.33 ng mL⁻¹ (S/N = 3). Furthermore, the developed method could facilitate the detection of SEB effectively in milk samples.

A new competitive aptasensor combined with HCR was developed for SEB detection.

Highly specific real-time quantification of diverse microRNAs in human samples using universal primer set frame

In this study, one group of universal primer set frame, composed by one reverse transcription (RT) primer frame and a pair of quantitative real-time polymerase chain reaction (qRT-PCR) primer frames, was elaborately screened and designed by homebuilt software for sensitive and specific quantification of diverse miRNAs. The universal primer set frame can be applied for multiplex miRNAs detection by simply changing the RT-X part of RT primer frame and RP-Y part of qRT-PCR reverse primer frame based on target sequence. The maximum similarity of RT-Y, RT-Z and qRT-PCR forward primer to the human genome and human transcriptome is less than 76%, ensuring the high specificity in human sample detection. The high sensitivity and broad dynamic linear range of the developed approaches by using designed primer set frame were demonstrated on the in vitro detection of miR-21 and miR-155, with dynamic range of 10 fM to 10 nM and detection limit of 3.74 × 10^-15 M and 5.81 × 10^-15 M for miR-21 and miR-155, respectively. In particular, the developed assays also have high sequence specificity which could clearly discriminate a single base difference in miRNA sequence. The contents of miR-21 and miR-155 in tissue and serum samples have been successfully detected using the developed assays. Results indicated that miR-21 and miR-155 were elevated in cancer tissue and serum specimens than that of normal samples, implying the developed assays hold a great promise for further application in biomedical research and early clinical diagnosis. More importantly, the primer set frame can be universally used in any miRNA investigation.

Colorimetric theophylline aggregation assay using an RNA aptamer and non-crosslinking gold nanoparticles

The authors are presenting a rapid method for the determination of theophylline using unique non-crosslinking gold nanoparticle (AuNP) aggregation. An RNA aptamer against theophylline is firstly split into two RNA fragments which then interact with bare AuNPs. The two RNA probes cause an enhancement of the salt tolerance of AuNPs. However, in the presence of theophylline, the RNA probes form a complex with theophylline so that less RNA probes are available to protect the AuNPs from salt-induced aggregation. Theophylline induced aggregation of AuNPs is accompanied by a color change from red to blue. The color change can be detected visually and via UV-vis absorptiometry by ratioing the absorbances at 650 and 520 nm. The ratio increases linearly in the 0.1 to 20 μM theophylline concentration range, with a 67 nM limit of detection. The method is highly sensitive and selective. Graphical abstract Single-stranded split RNA aptamers (R1 and R2) protect gold nanoparticles (AuNPs) from salt-induced non-crosslinking aggregation. After recognition of theophylline by the RNA probe, the unprotected AuNPs aggregate and undergo a color change from red to blue, and this is used to quantify the theophylline concentration.

Linear Chain Formation of Split-Aptamer Dimers on Surfaces Triggered by Adenosine

The detection of small molecules impacts various fields; however, their small size and low concentration are usually the cause of limitations in their detection. Thus, the need for biosensors with appropriate probes and signal amplification strategies is required. Aptamers are appropriate probes selected specifically against small targets such as adenosine. The possibility to split aptamers in parts led to original amplification strategies based on sandwich assays. By combining the self-assembling of oligonucleotide dimers with split-aptamer dangling ends and a surface plasmon resonance imaging technique, we developed an original amplification approach based on linear chain formation in the presence of the adenosine target. In this article, on the basis of sequence engineering, we analyzed its performance and the effect of the probe grafting density on the length of the chains formed at the surface of the biosensor.

Rapid and PCR-free DNA Detection by Nanoaggregation-Enhanced Chemiluminescence

The aggregation of gold nanoparticles (AuNPs) is known to induce an enhancement of localized surface plasmon resonance due to the coupling of plasmonic fields of adjacent nanoparticles. Here we show that AuNPs aggregation also causes a significant enhancement of chemiluminescence in the presence of luminophores. The phenomenon is used to introduce a rapid and sensitive DNA detection method that does not require amplification. DNA probes conjugated to AuNPs were used to detect a DNA target sequence specific to the fungus Ceratocystis fagacearum, causal agent of oak wilt. The hybridization of the DNA target with the DNA probes results in instantaneous aggregation of AuNPs into nanoballs, leading to a significant enhancement of luminol chemiluminescence. The enhancement reveals a linear correlation (R2 = 0.98) to the target DNA concentration, with a limit of detection down to 260 fM (260 × 10-15 M), two orders of magnitude higher than the performance obtained with plasmonic colorimetry and absorption spectrometry of single gold nanoparticles. Furthermore, the detection can be performed within 22 min using only a portable luminometer.

Lateral flow nucleic acid biosensor for sensitive detection of microRNAs based on the dual amplification strategy of duplex-specific nuclease and hybridization chain reaction

MicroRNAs (miRNAs) constitute novel biomarkers for various diseases. Accurate and quantitative analysis of miRNA expression is critical for biomedical research and clinical theranostics. In this study, a method was developed for sensitive and specific detection of miRNAs via dual signal amplification based on duplex specific nuclease (DSN) and hybridization chain reaction (HCR). A reporter probe (RP), comprising recognition sequence (3’ end modified with biotin) for a target miRNA of miR-21 and capture sequence (5’ end modified with Fam) for HCR product, was designed and synthesized. HCR was initiated by partial sequence of initiator probe (IP), the other part of which can hybridize with capture sequence of RP, and was assembled by hairpin probes modified with biotin (H1-bio and H2-bio). A miR-21 triggered cyclical DSN cleavage of RP, which was immobilized to a streptavidin (SA) coated magnetic bead (MB). The released Fam labeled capture sequence then hybridized with the HCR product to generate a detectable dsDNA. This polymer was then dropped on lateral flow strip and positive result was observed. The proposed method allowed quantitative sequence-specific detection of miR-21 (with a detection limit of 2.1 fM, S/N = 3) in a dynamic range from 100 fM to 100 pM, with an excellent ability to discriminate differences in miRNAs. The method showed acceptable testing recoveries for the determination of miRNAs in serum.

An Affordable Microsphere-Based Device for Visual Assessment of Water Quality

This work developed a prototype of an affordable, long-term water quality detection device that provides a visual readout upon detecting bacterial contamination. This device prototype consists of: (1) enzyme-releasing microspheres that lyse bacteria present in a sample, (2) microspheres that release probes that bind the DNA of the lysed bacteria, and (3) a detector region consisting of gold nanoparticles. The probes bind bacterial DNA, forming complexes. These complexes induce aggregation of the gold nanoparticles located in the detector region. The nanoparticle aggregation process causes a red to blue color change, providing a visual indicator of contamination being detected. Our group fabricated and characterized microspheres made of poly (ε-caprolactone) that released lysozyme (an enzyme that degrades bacterial cell walls) and hairpin DNA probes that bind to regions of the Escherichiacoli genome over a 28-day time course. The released lysozyme retained its ability to lyse bacteria. We then showed that combining these components with gold nanoparticles followed by exposure to an E. coli-contaminated water sample (concentrations tested-10⁶ and 10⁸ cells/mL) resulted in a dramatic red to blue color change. Overall, this device represents a novel low-cost system for long term detection of bacteria in a water supply and other applications.

Dual functional Phi29 DNA polymerase-triggered exponential rolling circle amplification for sequence-specific detection of target DNA embedded in long-stranded genomic DNA

An exonucleolytic digestion-assisted exponential rolling circle amplification (RCA) strategy was developed for sensitive and sequence-specific detection of target DNA embedded in long-stranded genomic DNA. Herein, Phi29 DNA polymerase plays two important roles as exonuclease and polymerase. Long-stranded genomic DNAs can be broken into small DNA fragments after ultrasonication. The fragments that contain target DNA, hybridize with a linear padlock probe to trigger the formation of a circular RCA template. The tails protruding from the 3'-end of the target DNA sequences are then digested by the 3' → 5' exonuclease activity of Phi29 DNA polymerase even if they fold into a double-stranded structure. The digested DNA fragments can then initiate subsequent RCA reaction. RCA products, which are designed to fold into G-quadruplex structures, exponentially accumulate when appropriate nicking endonuclease recognition sites are introduced rationally into the RCA template. This method is demonstrated to work well for real genomic DNA detection using human pathogen Cryptococcus neoformans as a model. In addition, this work has two other important discoveries: First, the presence of a 3'-tail can protect the RCA primer from degradation by Phi29 DNA polymerase. Second, 3' → 5' exonucleolytic activity of Phi29 DNA polymerase can work for both single- and double-stranded DNA.

Nanopore biosensor for sensitive and label-free nucleic acid detection based on hybridization chain reaction amplification

A label-free nanopore biosensor for detection of DNA target is proposed utilizing hybridization chain reaction (HCR) strategy for signal amplification. The DNA target triggered HCR to form large DNA nanostructure inside the nanopore and out the nanopore membrane, which inducing the ionic current decrease effectively due to the blockage of the nanopore. The developed method achieves a desirable sensitivity of 30fM with a wide linear dynamic range from 0.1 to 10pM and demonstrated good application for real sample analysis. This work has great potential to be applied in the early diagnosis of gene-related diseases and provide a new paradigm for label-free nucleic acid amplification strategy in ultrasensitive nanopore biosensor.

Nanotechnology-Enhanced No-Wash Biosensors for in Vitro Diagnostics of Cancer

In vitro biosensors have been an integral component for early diagnosis of cancer in the clinic. Among them, no-wash biosensors, which only depend on the simple mixing of the signal generating probes and the sample solution without additional washing and separation steps, have been found to be particularly attractive. The outstanding advantages of facile, convenient, and rapid response of no-wash biosensors are especially suitable for point-of-care testing (POCT). One fast-growing field of no-wash biosensor design involves the usage of nanomaterials as signal amplification carriers or direct signal generating elements. The analytical capacity of no-wash biosensors with respect to sensitivity or limit of detection, specificity, stability, and multiplexing detection capacity is largely improved because of their large surface area, excellent optical, electrical, catalytic, and magnetic properties. This review provides a comprehensive overview of various nanomaterial-enhanced no-wash biosensing technologies and focuses on the analysis of the underlying mechanism of these technologies applied for the early detection of cancer biomarkers ranging from small molecules to proteins, and even whole cancerous cells. Representative examples are selected to demonstrate the proof-of-concept with promising applications for in vitro diagnostics of cancer. Finally, a brief discussion of common unresolved issues and a perspective outlook on the field are provided.

Ultrasensitive colorimetric detection of circulating tumor DNA using hybridization chain reaction and the pivot of triplex DNA

This work presents an amplified colorimetric biosensor for circulating tumor DNA (ctDNA), which associates the hybridization chain reaction (HCR) amplification with G-Quadruplex DNAzymes activity through triplex DNA formation. In the presence of ctDNA, HCR occurs. The resulting HCR products are specially recognized by one sequence to include one GGG repeat and the other containing three GGG repeats, through the synergetic effect of triplex DNA and asymmetrically split G-Quadruplex forming. Such design takes advantage of the amplification property of HCR and the high peroxidase-like catalytic activity of asymmetrically split G-Quadruplex DNAzymes by means of triplex DNA formation, which produces color signals in the presence of ctDNA. Nevertheless, in the absence of ctDNA, no HCR happens. Thus, no triplex DNA and G-Quadruplex structure is formed, producing a negligible background. The colorimetric sensing platform is successfully applied in complex biological environments such as human blood plasma for ctDNA detection, with a detection limit corresponding to 0.1 pM. This study unambiguously uses triplex DNA forming as the pivot to integrate nucleic acid amplification and DNAzymes for producing a highly sensitive signal with low background.

A simple and sensitive aptasensor for colorimetric detection of adenosine triphosphate based on unmodified gold nanoparticles

A simple and sensitive colorimetric aptasensor for rapid and facile detection of adenosine triphosphate (ATP) has been demonstrated here based on aptamer-based hairpin probes and unmodified gold nanoparticles (AuNPs). The hairpin probe is constructed by adding another five nucleotides to the 5'-end of an anti-ATP aptamer which can hybridize to nucleotides at the 3'-end of the aptamer, forming a hairpin-shaped structure. In the absence of ATP, the hairpin probes are rigid, and the AuNPs are susceptible to salt-induced aggregation. Conversely, upon binding with target ATP, the hairpin probes undergo conformational changes, forming aptamer-ATP complexes and exposing flexible ends which coat the surface of AuNPs to inhibit their aggregation in the high salt solution. Subsequently, a blue-to-red color change can be recognized by the naked eye. The aptasensor achieved selective responses toward ATP with a detection limit of 0.1μM, and exhibited high-quality detection performance in biological samples. In addition, this detection method is simple, rapid and cost-effective, holding great potential for further applications in point-of-care research.

DNA-mediated inhibition of peroxidase-like activities on platinum nanoparticles for simple and rapid colorimetric detection of nucleic acids

In this research, we found that the peroxidase-like activities of noncovalent DNA-Pt hybrid nanoparticles could be obviously blocked, when Pt nanoparticles (PtNPs) were synthesized in situ using DNA as a template. Moreover, this self-assembled synthetic process was very convenient and rapid (within few mintues), and the inhibition mediated by DNA was also very effective. First, by the paper-based analytical device (PAD) we found the catalytic activities of DNA-Pt hybrid nanoparticles exhibited a linear response to the concentration of DNA in the range from 0.0075 to 0.25µM. Then, with the magnetic bead isolated system and target DNA-induced hybridization chain reaction (HCR), we realized the specific target DNA analysis with a low detection of 0.228nM, and demonstrated its effectivity in distinguishing the target DNA from other interferences. To our knowledge, this is the first report that used the nanoassembly between DNA and PtNPs for colorimetric detection of nucleic acids, which was based on DNA-mediated inhibition of catalytic activities of platinum nanoparticles. The results may be useful for understanding the interactions between DNA and metal nanoparticles, and for development of other convenient and effective analytical strategies.

Intracellular DNA and microRNA sensing based on metal-organic framework nanosheets with enzyme-free signal amplification

A new fluorescent sensing platform based on ultrathin metal-organic framework (MOF) nanosheets (MnDMS) was prepared from the flexible ligand 2,2-dimethylsuccinate and Mn ions. The MnDMS nanoparticles can be obtained by simply ultrasonication of the MnDMS crystal, and then can be exfoliated into nanosheets by Li-intercalation method. The MnDMS nanosheets can be easily assembled with biological probes, leading to efficient fluorescence quenching of the fluorophore tagged ssDNA and microRNA (miRNA). By using a hybridization chain reaction (HCR) strategy, the fluorescence signal can be obviously amplified. A good linearity was obtained from 1 pM to 200 pM of target ssDNA, with a detection limit of 0.2 pM. The HCR/MnDMS system provides an effective way to monitor miRNA in living cells. Therefore, the MnDMS nanosheets can be used as a new kind of platform in biomedical sensing applications.

A colorimetric sensing platform based upon recognizing hybridization chain reaction products with oligonucleotide modified gold nanoparticles through triplex formation

A novel colorimetric sensing strategy for biomolecule assay has been developed, which integrates the signal amplification of the hybridization chain reaction (HCR) with the assembly of gold nanoparticles (AuNPs) through triplex formation. In the presence of targets, the HCR process can be triggered, the HCR products are specifically recognized by triplex-forming oligonucleotide (TFO) functionalized AuNPs, accompanying the aggregation of AuNPs and a dramatic absorbance change at 522 nm. In addition, the DNA hairpin probes can form rigid triplex structures with TFO-functionalized AuNPs in the absence of targets, resulting in a negligible background signal. By taking advantage of this new biosensor platform, a broad range of targets, involving nucleic acids, small molecules and proteins, have been successfully determined with high sensitivity and selectivity, which may hold great potential for practical application.

Hybridization chain reaction: a versatile molecular tool for biosensing, bioimaging, and biomedicine

This review provides a comprehensive overview of the fundamental principles, analysis techniques, and application fields of hybridization chain reaction and its development status.

Quantum material accompanied nonenzymatic cascade amplification for ultrasensitive photoelectrochemical DNA sensing

A novel cascade photoelectrochemical (PEC) signal amplification sensing strategy was designed and applied in target DNA detection by introducing quantum dots (QD) as the accompanying tag.

Enzyme-free, signal-amplified nucleic acid circuits for biosensing and bioimaging analysis

Enzyme-free, signal-amplified nucleic acid circuits utilize programmed assembly reactions between nucleic acid substrates to transduce a chemical input into an amplified detection signal.