Fluorescence resonance energy transfer-based hybridization chain reaction for in situ visualization of tumor-related mRNA

Mechanism study of Dual-Emission ratiometric fluorescent pH-Sensitive carbon quantum dots and its application on mornitoring enzymatic catalysis

Carbon dots (CQD) have received significant attention as a novel ratiometric fluorescent pH nanoprobe, owing to their favorable optical properties and excellent biocompatibility. Despite their appealing features, the precise mechanism behind the pH-sensitive photoluminescence of CQDs remains to be fully understood. This study endeavors to unravel the mechanism underlying the pH-responsive ratiometric fluorescence in dual-emission CQDs, synthesized through a one-step hydrothermal method using o-phenylenediamine and oxalic acid as precursors. The resultant CQDs exhibit inherent dual-emission at wavelengths of 383 nm and 566 nm, with the ratiometric fluorescence response tailored by the ratio of precursors, providing a robust tool for pH sensing across a range of 2 to 6. Detailed characterizations, including chemical, morphological, and optical analyses, alongside theoretical insights from time-dependent density functional theory (TD-DFT), elucidate the mechanism underlying the pH-dependent luminescence, attributed to the electron cloud transmission between amide and adjacent carboxyl groups on the CQD surface. The superior performance of these CQDs in real-time pH monitoring is demonstrated through their application in glucose oxidase-catalyzed reactions, showcasing their potential as efficient, reliable nanoprobes for biomedical research and diagnostic applications.

A novel viral RNA detection method based on the combined use of trans-acting ribozymes and HCR-FRET analyses

The diagnoses of retroviruses are essential for controlling the rapid spread of pandemics. However, the real-time Reverse Transcriptase quantitative Polymerase Chain Reaction (RT-qPCR), which has been the gold standard for identifying viruses such as SARS-CoV-2 in the early stages of infection, is associated with high costs and logistical challenges. To innovate in viral RNA detection a novel molecular approach for detecting SARS-CoV-2 viral RNA, as a proof of concept, was developed. This method combines specific viral gene analysis, trans-acting ribozymes, and Fluorescence Resonance Energy Transfer (FRET)-based hybridization of fluorescent DNA hairpins. In this molecular mechanism, SARS-CoV-2 RNA is specifically recognized and cleaved by ribozymes, releasing an initiator fragment that triggers a hybridization chain reaction (HCR) with DNA hairpins containing fluorophores, leading to a FRET process. A consensus SARS-CoV-2 RNA target sequence was identified, and specific ribozymes were designed and transcribed in vitro to cleave the viral RNA into fragments. DNA hairpins labeled with Cy3/Cy5 fluorophores were then designed and synthesized for HCR-FRET assays targeting the RNA fragment sequences resulting from ribozyme cleavage. The results demonstrated that two of the three designed ribozymes effectively cleaved the target RNA within 10 minutes. Additionally, DNA hairpins labeled with Cy3/Cy5 pairs efficiently detected target RNA specifically and triggered detectable HCR-FRET reactions. This method is versatile and can be adapted for use with other viruses. Furthermore, the design and construction of a DIY photo-fluorometer prototype enabled us to explore the development of a simple and cost-effective point-of-care detection method based on digital image analysis.

Dual-Function DNA Nanowires with Self-Feedback Amplification and Efficient Signal Transduction for Intracellular Imaging of MicroRNA-155

Intracellular detection and imaging of microRNAs (miRNAs) with low expression usually face the problem of unsatisfactory sensitivity. Herein, a novel dual-function DNA nanowire (DDN) with self-feedback amplification and efficient signal transduction was developed for the sensitive detection and intracellular imaging of microRNA-155 (miRNA-155). Target miRNA-155 triggered catalytic hairpin assembly (CHA) to generate plenty of double-stranded DNA (dsDNA), and a trigger primer exposed in dsDNA initiated a hybridization chain reaction (HCR) between four well-designed hairpins to produce DDN, which was encoded with massive target sequences and DNAzyme. On the one hand, target sequences in DDN acted as self-feedback amplifiers to reactivate cascaded CHA and HCR, achieving exponential signal amplification. On the other hand, DNAzyme encoded in DDN acted as signal transducers, successively cleaving Cy5 and BHQ-2 labeled substrate S to obtain a significantly enhanced fluorescence signal. This efficient signal transduction coupling self-feedback amplification greatly improved the detection sensitivity with a limit of detection of 160 aM for miRNA-155, enabling ultrasensitive imaging of low-abundance miRNA-155 in living cells. The constructed DDN creates a promising fluorescence detection and intracellular imaging platform for low-expressed biomarkers, exhibiting tremendous potential in biomedical studies and clinical diagnosis of diseases.

Integration of Hybridization Chain Reaction and Protein-Binding Amplification for Long-Term Imaging of Intracellular mRNA: Avoiding Signal Fluctuation

Amplified nanoprobes based on hybridization chain reaction (HCR) have been widely developed for the detection of intracellular low abundance mRNA. However, the formed chain-like assembly decorated with fluorophore would be degraded rapidly by endogenous enzyme, resulting in failure of the long-term fluorescence imaging. To address this issue, herein, a composite signal-amplifying strategy that integrates HCR into protein-binding signal amplification (HPSA) was communicated for the in situ imaging of mRNA by avoiding signal fluctuation. Different from conventional HCR-based nanoprobes (HCR-nanoprobe), the HCR was used as the signal-triggered mode and the amplifying signal generated from in situ fluorophore-protein binding in cells, which can maintain high stability of the signal for a long time. As a proof-of-principle, a nanobeacon based on HPSA (HPSA-nanobeacon) was constructed to detect TK1 mRNA. Taking advantage of the double signal-amplifying mode, the endogenous TK1 mRNA was sensitively detected and the fluorescence signal was maintained for more than 8 h in HepG2 cells. The attempt in this work provides a new option to the current signal-amplifying strategy for sensing nucleic acid targets with high stability, significantly enhancing the acquisition of intracellular molecular information.

Strand displacement-triggered FRET nanoprobe tracking TK1 mRNA in living cells for ratiometric fluorimetry of nucleic acid biomarker

A precisely designed dual-color biosensor has realized a visual assessment of thymidine kinase 1 (TK1) mRNA in both living cells and cell lysates. The oligonucleotide probe is constructed by hybridizing the antisense strand of the target and two recognition sequences, in which FAM serves as the donor and TAMRA as the acceptor. Once interacting with the target, two recognition strands are replaced, and then the antisense complementary sequence forms a more stable double-stranded structure. Due to the increasing spatial distance between two dyes, the FRET is attenuated, leading to a rapid recovery of FAM fluorescence and a reduction of TAMRA fluorescence. A discernible color response from orange to green could be observed by the naked eye, with a limit of detection (LOD) of 0.38 nM and 5.22 nM for spectrometer- and smartphone-based assays, respectively. The proposed ratiometric method transcends previous reports in its capacities in visualizing TK1 expression toward reliable nucleic acid biomarker analysis, which might establish a general strategy for ratiometric biosensing via strand displacement.

Single-Cell Imaging of mRNA by Target RNA-Initiated RCA

We present a powerful method for direct mRNA detection based on ligation-based recognition and in situ amplification, capable of single-cell imaging mRNA at single-nucleotide and single-molecule resolution. Attributed to the use of Splint R ligase that can ligate padlock probe with RNA as target template, this method can efficiently detect mRNA in the absence of reverse transcription. This method enables spatial localization and correlation analysis of gene expression in single cells, which helps us to elucidate gene function and regulatory mechanisms.

Recent advances in cascade isothermal amplification techniques for ultra-sensitive nucleic acid detection

Nucleic acid amplification techniques have always been one of the hot spots of research, especially in the outbreak of COVID-19. From the initial polymerase chain reaction (PCR) to the current popular isothermal amplification, each new amplification techniques provides new ideas and methods for nucleic acid detection. However, limited by thermostable DNA polymerase and expensive thermal cycler, PCR is difficult to achieve point of care testing (POCT). Although isothermal amplification techniques overcome the defects of temperature control, single isothermal amplification is also limited by false positives, nucleic acid sequence compatibility, and signal amplification capability to some extent. Fortunately, efforts to integrating different enzymes or amplification techniques that enable to achieve intercatalyst communication and cascaded biotransformations may overcome the corner of single isothermal amplification. In this review, we systematically summarized the design fundamentals, signal generation, evolution, and application of cascade amplification. More importantly, the challenges and trends of cascade amplification were discussed in depth.

Rapid Visible Detection of African Swine Fever Virus Using Hybridization Chain Reaction-Sensitized Magnetic Nanoclusters and Affinity Chromatography

African swine fever virus (ASFV) is a severe and persistent threat to the global swine industry. As there are no vaccines against ASFV, there is an immense need to develop easy-to-use, cost-effective, and rapid point-of-care (POC) diagnostic platforms to detect and prevent ASFV outbreaks. Here, a novel POC diagnostic system based on affinity column chromatography for the optical detection of ASFV is presented. This system employs an on-particle hairpin chain reaction to sensitize magnetic nanoclusters with long DNA strands in a target-selective manner, which is subsequently fed into a column chromatography device to produce quantitatively readable and colorimetric signals. The detection approach does not require expensive analytical apparatus or immobile instrumentation. The system can detect five genes constituting the ASFV whole genome with a detection limit of ≈19.8 pm in swine serum within 30 min at laboratory room temperature. With an additional pre-amplification step using polymerase chain reaction (PCR), the assay is successfully applied to detect the presence of ASFV in 30 suspected swine samples with 100% sensitivity and specificity, similar to quantitative PCR. Thus, this simple, inexpensive, portable, robust, and customizable platform for the early detection of ASFV can facilitate the timely surveillance and implementation of control measures.

Recent progress in the development of DNA-based biosensors integrated with hybridization chain reaction or catalytic hairpin assembly

As isothermal, enzyme-free signal amplification strategies, hybridization chain reaction (HCR) and catalytic hairpin assembly (CHA) possess the advantages such as high amplification efficiency, excellent biocompatibility, mild reactions, and easy operation. Therefore, they have been widely applied in DNA-based biosensors for detecting small molecules, nucleic acids, and proteins. In this review, we summarize the recent progress of DNA-based sensors employing typical and advanced HCR and CHA strategies, including branched HCR or CHA, localized HCR or CHA, and cascaded reactions. In addition, the bottlenecks of implementing HCR and CHA in biosensing applications are discussed, such as high background signals, lower amplification efficiency than enzyme-assisted techniques, slow kinetics, poor stability, and internalization of DNA probes in cellular applications.

Detection of Hepatitis C virus RNA using a novel hybridization chain reaction method that competitively dampens cascade amplification

The hybridization chain reaction (HCR) is widely used for biosensing. However, HCR does not provide the required sensitivity. In this study, we reported a method to improve the sensitivity of HCR by dampening the cascade amplification. First, we designed a biosensor based on HCR, and an initiator DNA was used to trigger the cascade amplification. Optimization of the reaction was then performed, and the results showed that the limit of detection (LOD) for the initiator DNA was about 2.5 nM. Second, we designed a series of inhibitory DNAs to dampen the HCR cascade amplification, and DNA dampeners (50 nM) were applied in the presence of the DNA initiator (50 nM). One of the DNA dampeners (D5) showed the best inhibitory efficiency of greater than 80%. This was further applied at concentrations ranging from 0 nM to 10 nM to prohibit the HCR amplification caused by a 2.5 nM initiator DNA (the limit of detection for this initiator DNA). The results showed that 0.156 nM of D5 could significantly inhibit the signal amplification (p<0.05). Additionally, the limit of detection for the dampener D5 was 16 times lower than that for the initiator DNA. Based on this detection method, we achieved a detection limit as low as 0.625 nM for HCV-RNAs. In summary, we developed a novel method with improved sensitivity to detect the target designed to prohibit the HCR cascade. Overall, this method could be used to qualitatively detect the presence of single-stranded DNA/RNA.

Sensitive Detection of Salmonella Based on CRISPR-Cas12a and the Tetrahedral DNA Nanostructure-Mediated Hyperbranched Hybridization Chain Reaction

Salmonella severely threatens global human health and causes financial burden. The ability to sensitively detect Salmonella in food samples is highly valuable but remains a challenge. Herein, a sensitive detection method for Salmonella was developed by coupling immunomagnetic separation with the CRISPR-Cas12a system and the tetrahedral DNA nanostructure-mediated hyperbranched hybridization chain reaction (TDN-hHCR). In the detection system, the target Salmonella was immunomagnetically separated and labeled with bio-barcode DNA-modified gold nanoparticles (AuNPs), which could transfer and magnify the signal of a bacterial cell into numerous bio-barcode DNA molecules. Afterward, the bio-barcode DNA can trigger the trans-cleavage activity of CRISPR-Cas12a to inhibit the process of the TDN-hHCR to generate a fluorescence readout. Due to the high immunomagnetic separation efficiency and the effective signal amplification of CRISPR-Cas12a and the TDN-hHCR, Salmonella as low as 8 CFU/mL could be easily detected. Meanwhile, this has been applied for practical use and showed the capability to detect 17 and 25 CFU/mL in spiked milk and egg white, respectively, indicating its potential application in real samples.

Control of Enzyme Reaction Initiation inside Giant Unilamellar Vesicles by the Cell-Penetrating Peptide-Mediated Translocation of Cargo Proteins

Cell-penetrating peptides (CPPs) play important roles in directly delivering biomolecules, such as DNA, proteins, and peptides, into living cells. In artificial lipid membranes, such as planar lipid bilayers, the direct membrane translocation of β-galactosidase via Pep-1 (one of the CPPs) is dependent upon a voltage gradient between the inner and outer leaflets of the lipid membranes. Giant unilamellar vesicles (GUVs) with asymmetric lipid distributions, which are recently generated using microfluidic technologies, can be observed by optical microscopy. Therefore, interactions between CPPs and asymmetric lipid bilayers in different kinds of lipids and the translocation mechanism of proteins via CPPs into GUVs can be investigated at the level of a single asymmetric GUV. This CPP-based system for transporting proteins into GUVs will be applied to control the start of enzyme reactions in GUVs. This study aimed to explore efficient protein translocation into GUVs via CPP and demonstrate that enzymatic reactions start in GUVs using a CPP-mediated direct translocation. The interactions and the enzyme reactions between the CPP (Pep-1 or penetratin)-DNase I complexes and the asymmetric or symmetric GUV membranes containing the negatively or neutrally charged lipids were observed by confocal laser-scanning microscopy. The asymmetric GUVs containing phosphatidylserine (PS) in the inner leaflet showed efficient DNase I translocation into GUVs via penetratin. Finally, the formation of a cross-linked actin network was observed in asymmetric PS GUVs incubated with Pep-1-streptavidin complexes. The CPP-mediated direct translocation can contribute to developing artificial cell models with the capacity to control the initiation of enzymatic reactions.

Cationic Copolymer-Augmented DNA Hybridization Chain Reaction

Various DNA assembly techniques and structures have emerged with the continuous progress of DNA nanotechnology. DNA hybridization chain reaction (HCR) is a representative example owing to isothermal and enzyme-free features. However, HCR is time consuming and is inhibited by nucleases present in biological samples. Herein, we demonstrated that a cationic copolymer, poly(l-lysine)-graft-dextran (PLL-g-Dex), significantly facilitated HCR and increased its initiator sensitivity by 40-fold. PLL-g-Dex promoted the generation of HCR products with high molecular weight by accelerating the initiation and the subsequent growth steps of HCR. Moreover, PLL-g-Dex protected the HCR system from nucleases, permitting HCR in the presence of serum components. Addition of PLL-g-Dex is a universal and efficient strategy that does not require optimization of the reactor setup or DNA sequences, thus laying a solid foundation for the wider application of HCR.

Smart Hairpins@MnO2 Nanosystem Enables Target-Triggered Enzyme-Free Exponential Amplification for Ultrasensitive Imaging of Intracellular MicroRNAs in Living Cells

Sensitive and specific imaging of microRNA (miRNA) in living cells is of great value for disease diagnosis and monitoring. Hybridization chain reaction (HCR) and DNAzyme-based methods have been considered as powerful tools for miRNA detection, with low efficient intracellular delivery and limited amplification efficiency. Herein, we propose a Hairpins@MnO₂ nanosystem for intracellular enzyme-free exponential amplification for miRNA imaging. The enzyme-free exponential amplification is based on the synergistic cross-activation between HCR and DNAzymes. The MnO₂ nanosheets were employed as the carrier of three kinds of hairpin DNA probes and further provided appropriate Mn²⁺ as DNAzyme cofactors in the living cell. Upon entering cells and in the presence of highly expressed glutathione (GSH) in tumors, MnO₂ is reduced to release Mn²⁺ and the three kinds of hairpin DNA probes. In the presence of target miRNA, the released hairpin DNA H1 and H2 probes self-assemble via HCR into the wire-shaped active Mn²⁺-based DNAzymes which further catalyze the cleavage of H3 to generate numerous new triggers to reversely stimulate HCR amplifiers, thus offering tremendously amplified Förster resonance energy transfer readout. The method has a detection limit of 33 fM, which is 2.4 × 10⁴ times lower than that of the traditional HCR system. The developed method also has a high specificity; even miRNAs with a single base difference can be distinguished. Live cell imaging experiments confirmed that this Hairpins@MnO₂ nanosystem allows accurate differentiation of miRNA expression of cancer cells and normal cells. The method holds great potential in biological research of nucleic acids.

Ratiometric fluorescence resonance energy transfer for reliable and sensitive detection of intracellular telomerase RNA via strand displacement reaction amplification

Human telomerase RNA (hTR) is one essential component of telomerase and is overexpressed in tumor cells. Therefore, the reliable and sensitive detection of hTR is essential for the early cancer diagnosis. Herein, to avoid the false positive signals caused by co-existing components in the cell, a ratiometric fluorescence resonance energy transfer (FRET) strategy was developed to achieve reliable detection of intracellular hTR. Manganese dioxide nanosheets (MnO₂NS) with good biocompatibility carry two fluorophore-labelled hairpin DNA probes into the cancer cell and then release the probes via decomposition of MnO₂NS by intracellular L-glutathione reduced (GSH). Then, hTR triggered the cyclic strand displacement reaction (SDR) between two hairpin DNA probes to continuously form DNA duplexes, which made two fluorophores close to each other and led to an effective FRET. Fluorescence imaging demonstrated a higher expression level of hTR in HeLa cells than that in normal HL-7702 cells. The high specificity of hairpin DNA probes and SDR make it easy to discriminate the single-base mutation. Therefore, it provides a highly sensitive, simple and reliable method for the extracellular and intracellular detection of hTR.

An entropy-driven signal-off DNA circuit for label-free, visual detection of small molecules with enhanced accuracy

An entropy-driven DNA circuit offers an efficient means of sensitive analyte detection with signal amplification. In this article, we rationally engineered an aptamer-based entropy-driven signal-off DNA circuit for colorimetric detection of small molecules. The proposed signal-off DNA circuit is activated by target small molecule binding to drive the collapse of G-quadruplex DNAzyme, accompanied by the colour change of the detection solution from dark blue to light blue. Entropy-driven recycling hybridization significantly magnified the input signal of the target small molecule. Such an assay enables naked-eye detection of adenosine triphosphate and oxytetracycline at concentrations as low as 0.5 μM and 1 μM respectively. Moreover, when compared with the signal-on DNA circuit, the entropy-driven signal-off DNA circuit for colorimetric detection has two advantages. Firstly, unlike in the signal-on DNA circuit, the unavoidable formation of waste complexes in the absence of a target in the signal-off DNA circuit has no influence on target detection performance as its background signal is only determined by the substrate complex. Secondly, the signal-on DNA circuit cannot distinguish false-positive signals generated by invasive catalysts (e.g., HRP, serum, Fe₃O₄), while the signal-off DNA circuit can distinguish those signals as undesired signals. Overall, the signal-off DNA circuit affords a novel strategy for sensitive and accurate detection of small molecules.

A novel FRET-based dendritic hybridization chain reaction for tumour-related mRNA imaging

A novel FRET-based dendritic hybridization chain reaction (D-HCR) for TK1 mRNA imaging in living cells was developed. Compared with traditional complex D-HCR methods, it includes the advantages of having a simple design, an accurate signal and is suitable for use with living cells.

Recent Progress in DNA Hybridization Chain Reaction Strategies for Amplified Biosensing

With the continuous development of DNA nanotechnology, various spatial DNA structures and assembly techniques emerge. Hybridization chain reaction (HCR) is a typical example with exciting features and bright prospects in biosensing, which has been intensively investigated in the past decade. In this Spotlight on Applications, we summarize the assembly principles of conventional HCR and some novel forms of linear/nonlinear HCR. With advantages like great assembly kinetics, facile operation, and an enzyme-free and isothermal reaction, these strategies can be integrated with most mainstream reporters (e.g., fluorescence, electrochemistry, and colorimetry) for the ultrasensitive detection of abundant targets. Particularly, we select several representative studies to better illustrate the novel ideas and performances of HCR strategies. Theoretical and practical utilities are confirmed for a range of biosensing applications. In the end, a deep discussion is provided about the challenges and future tasks of this field.

Imaging of Cancer Cells and Dictated Cytotoxicity Using Aptamer-Guided Hybridization Chain Reaction (HCR)-Generated G-Quadruplex Chains

DNA nanotechnology provides powerful tools for developing cancer theranostics. Here we introduce the autonomous surface-nucleolin-guided HCR that leads to the polymerization of G-quadruplex polymer chains, in which the Zn^II -protoporphyrin IX is intercalated. We demonstrate that MDA-MB-231 (Triple Negative Breast Cancer cells, TNBC) with overexpressed surface nucleolin were able to induce HCR leading to the formation of the Zn^II PPIX-loaded G-quadruplex polymer chains, while the M10 epithelial breast cells served as control. The Zn^II PPIX-loaded nanowires allow the selective imaging of TNBC, and their permeation into the TNBC leads to selective cytotoxicity and guided photodynamic therapy toward the cancer cells due to structural perturbation of the membranes. The aptamer-guided HCR-generated G-quadruplex polymer chains may serve as a versatile tool to target TNBC featuring poor prognosis and high pathological risk of recurrence, thus offering a promising theranostic platform.

Portable microfluidic device with thermometer-like display for real-time visual quantitation of Cadmium(II) contamination in drinking water

Cadmium (Cd²⁺) is a toxic metal ion widely existing in water, soil and food. Conventional water quality control heavily relies on expensive, bulky and sophisticated instrument such as spectrometry, which is time-consuming and incompatible with on-site, real-time detection. Here, a portable microfluidic device with thermometer-like visual readouts is developed for real-time quantitation of cadmium (II) contamination in drinking water. We use Cd²⁺-dependent DNAzyme (Cd16), which is cleaved when Cd²⁺ is present, creating a single strand DNA which triggers catalytic hairpin assembly (CHA) with two hairpins H1 and H2 as the building blocks. Plenty of H1H2 complex, the product after the Cd²⁺-mediated CHA, are generated, which can connect magnetic microparticles (MMPs) and polystyrene microparticles (PMPs), forming "MMPs-H1H2-PMPs" sandwich structure. To provide visual readout to quantitate the particle connection, the particle solution is loaded into a portable microfluidic chip. A magnetic separator first removes MMPs and the connected PMPs, while free PMPs can continue flowing until accumulating into a bar at the particle dam. Shown as a thermometer-like display, the accumulating length is inversely proportional to the concentration of Cd²⁺, enabling quantitative detection of Cd²⁺ by the naked eye. The proposed device exhibits a limit of detection of 11.3 nM of Cd²⁺, selectivity >200-fold against other metal ions, high tolerance to the interferents present in drinking water and high recovery rate in tap water. With high analytical performance without any sample preparation step, this portable device is highly promising in real-time monitoring in urban drinking water at sites.

Hairpin DNA-Mediated isothermal amplification (HDMIA) techniques for nucleic acid testing

Nucleic acid detection is of great importance in a variety of areas, from life science and clinical diagnosis to environmental monitoring and food safety. Unfortunately, nucleic acid targets are always found in trace amounts and their response signals are difficult to be detected. Amplification mechanisms are then practically needed to either duplicate nucleic acid targets or enhance the detection signals. Polymerase chain reaction (PCR) is one of the most popular and powerful techniques for nucleic acid analysis. But the requirement of costly devices for precise thermo-cycling procedures in PCR has severely hampered the wide applications of PCR. Fortunately, isothermal molecular reactions have emerged as promising alternatives. The past decade has witnessed significant progress in the research of isothermal molecular reactions utilizing hairpin DNA probes (HDPs). Based on the nucleic acid strand interaction mechanisms, the hairpin DNA-mediated isothermal amplification (HDMIA) techniques can be mainly divided into three categories: strand assembly reactions, strand decomposition reactions, and strand creation reactions. In this review, we introduce the basics of HDMIA methods, including the sensing principles, the basic and advanced designs, and their wide applications, especially those benefiting from the utilization of G-quadruplexes and nanomaterials during the past decade. We also discuss the current challenges encountered, highlight the potential solutions, and point out the possible future directions in this prosperous research area.

Toehold-mediated ligation-free rolling circle amplification enables sensitive and rapid imaging of messenger RNAs in situ in cells

In situ analysis of tumor-related messenger RNAs (mRNAs) is significant in identifying cancer cells at the genetic level in the early stage. Rolling circle amplification (RCA)-based methods are primary tools for in situ mRNA assay, however, the necessary ligation reaction not only shows low ligation efficiency, but also greatly prolongs the assay time that increases the risk of cells losing and mRNAs leakage. In this work, we propose a novel toehold-mediated ligation-free RCA (TMLFRCA) on a designed structure-switchable dumbbell-shaped probe (SDP). Target mRNA can specifically activate SDP from its circular form by toehold strand displacement, thereby initiates in situ RCA for mRNA imaging with the help of a short DNA primer. For the proof-of-concept demonstration, the TK1 mRNA was sensitively detected by TMLFRCA in less than 3.5 h with a limit of detection (LOD) of 0.39 fM (corresponds to 2.39×10⁸copiesL^-1), and significantly improved specificity capable for distinguishing single base difference. The sensitivity of the TMLFRCA for TK1 mRNA in situ assay is ∼29-fold and ∼7-fold higher than that of FISH and ligase-assisted RCA method, respectively, which enables the TMLFRCA method capability of highly sensitive and specific distinction mRNA expression levels between cancer cells and normal cells. We believe this TMLFRCA strategy would be of great value in both basic research and clinical diagnosis.

mRNA-Activated Multifunctional DNAzyme Nanotweezer for Intracellular mRNA Sensing and Gene Therapy

Deoxyribozyme (DNAzyme) is regarded as a promising gene therapy drug. However, poor cellular uptake efficacy and low biological stability limit the utilization of DNAzyme in gene therapy. Here, we report a well-known programmable DNAzyme-based nanotweezer (DZNT) that provides a new strategy for the detection of TK1 mRNA and survivin mRNA-targeted gene silencing therapy. At the end of the DZNT arm, there are two functionalized single-stranded DNA and each consists of two parts: the segment complementary to TK1 mRNA and the split-DNAzyme segment. The hybridization with intracellular TK1 mRNA enables the imaging of TK1 mRNA. Meanwhile, the hybridization draws the split-DNAzyme close to each other and activates DNAzyme to cleave the survivin mRNA to realize gene silencing therapy. The results demonstrate that the DZNT nanocarrier has excellent cell penetration, good biocompatibility, and noncytotoxicity. DZNT can image intracellular biomolecule TK1 mRNA with a high contrast. Furthermore, the split-DNAzyme can efficiently cleave the survivin mRNA with the aid of TK1 mRNA commonly present in cancer cells, accordingly can selectively kill cancer cells, and has no harm to normal cells. Taken together, the multifunctional programmable DZNT provides a promising platform for the early diagnosis of tumors and gene therapy.

Sensitive detection of intracellular telomerase activity via double signal amplification and ratiometric fluorescence resonance energy transfer

As an important and universal tumor marker, the reliable and in situ detection of intracellular telomerase activity is crucial for cancer diagnosis. Herein, a ratiometric fluorescence resonance energy transfer (FRET) method was developed for detecting intracellular telomerase activity. It takes full advantage of manganese dioxide nanosheets (MnO2NS) that can carry DNA probes with different conformations into cells and then completely release the DNA probes via decomposition of MnO2NS by intracellular reduced glutathione (GSH). In the presence of telomerase, a telomere substrate (TS) could be extended to form long telomerase extension products (TEPs), which trigger the cycling strand displacement reaction (SDR) between two fluorophore-labeled hairpin DNA probes to form lots of DNA duplexes. The close contact of two fluorophores led to an effective ratiometric FRET for reliable detection of telomerase activity. Fluorescence confocal imaging demonstrated that the activity of telomerase in tumor cells was reliably detected. The inhibition of telomerase activity by an inhibitor resulted in a decrease in FRET signal. For extracellular detection, the FRET ratio (FA/FD) shows a good linear relationship with the number of HeLa cells in the range of 20-1000 cells. Therefore, it offers a more facile method for reliable and sensitive detection of intracellular telomerase activity.

The Recent Development of Hybridization Chain Reaction Strategies in Biosensors

With the continuous development of biosensors, researchers have focused increasing attention on various signal amplification strategies to pursue superior performance for more applications. In comparison with other signal amplification strategies, hybridization chain reaction (HCR) as a powerful signal amplification technique shows its certain charm owing to nonenzymatic and isothermal features. Recently, on the basis of conventional HCR, this technique has been developed and improved rapidly, and a variety of HCR-based biosensors with excellent performance have been reported. Herein, we present a systematic and critical review on the research progress of HCR in biosensors in the last five years, including the newly developed HCR strategies such as multibranched HCR, migration HCR, localized HCR, in situ HCR, netlike HCR, and so on, as well as the combination strategies of HCR with isothermal signal amplification techniques, nanomaterials, and functional DNA molecules. By illustrating some representative works, we also summarize the advantage and challenge of HCR in biosensors, and offer a deep discussion of the latest progress and future development trends of HCR in biosensors.

Enzyme-free electrochemical biosensor based on amplification of proximity-dependent surface hybridization chain reaction for ultrasensitive mRNA detection

The ability to recognize mRNA with high efficiency in cells would greatly facilitate the elucidation of mRNA-mediated cellular cascades and their disease associations. However, most traditional electrochemical strategies targeting nucleotides are always confronted with cumbersome interface operation and washing procedures, as well as the high cost of labeling and the strict reaction conditions of tool enzymes, limiting their potential applications. To address these issues, herein we reported, for the first time, a simple label-free, isothermal, non-enzymatic, and ultrasensitive homogeneous electrochemical biosensor based on autonomous proximity-dependent surface hybridization chain reaction (HCR), for sensitive signal amplification and highly specific detection of target survivin mRNA with a detection limit of 3 fM. The target triggers hybridization chain reaction and mRNA-fueled surface hybridization of ferrocene-tagged metastable DNA hairpin probes on proximity-dependent surface hybridization, resulting in the formation of multiple long-range duplex DNA chains which are immobilized onto the gold electrodes with a substantially stable ferrocene-mediated redox current. Thus, a significant electrochemical signal increase is observed dependent on the concentration of the target RNA, with a very low detection limit. Mo-reover, this molecular biosensor also exhibits excellent specificity to distinguish even single base mismatched, with strong reliability. The developed biosensor provides a novel promising tool for ultra-sensitive and selective detection, and it has great potential to be applied in mRNA-related biochemical research and clinical cancer diagnostics in more detail.

Amplified AND logic platform for cell identification

Herein, we developed an amplified AND logic platform (AALP) on a cell membrane, which integrated two DNA aptamers for cell recognition and localized catalytic hairpin assembly (LCHA) for signal amplification. The AALP could perform "AND" logic computing via a double-checked strategy of two biomarkers on similar cell surfaces and precisely label the target cells with an amplified fluorescence signal.

Self-Assembled mRNA-Responsive DNA Nanosphere for Bioimaging and Cancer Therapy in Drug-Resistant Cells

DNA assembly has provided new opportunities for the development of a novel drug delivery system (DDS) for real-time monitoring and precision treatment of cancer lesions. Herein, we propose mRNA-responsive DNA nanospheres (DNA-NS), whose self-assembly can be triggered by products of rolling circle amplification and functional hairpins and deliver anticancer drug doxorubicin (DOX) for bioimaging and cancer therapy. It has been demonstrated that DNA-NS exhibited good stability in biological environments. Hence, DNA-NS can serve as a universal platform of detections of mRNA related to various tumor cells. DNA-NS can also be applied in the mRNA-dependent DDS. For drug-resistant cells, which are widely present in actual cancer models, DNA-NS can effectively overcome the efflux action of drug-resistant cells to improve the therapeutic efficacy of DOX. In summary, this study provides a potential strategy for constructing the endogenous mRNA-responsive DDS for cancer diagnosis and chemotherapy in vivo.

Targeted and direct intracellular delivery of native DNAzymes enables highly specific gene silencing

DNAzymes exhibit high potential as gene silencing agents for therapeutic applications. Such purposes, however, are significantly challenged by the targeted and successful delivery of unmodified DNAzymes into cells with minimal side effects. Here, we set out to formulate and demonstrate a new stimuli-responsive and constrained aptamer/DNAzyme (Apt/Dz) catenane nanostructure for highly specific gene silencing. The rational design of the Apt/Dz catenane nanostructure with the respective integration of the aptamer sequence and the completely closed catenane format enables both the targeted capability and significantly improved nuclease resistance, facilitating the stable and targeted delivery of unmodified Dz into cancer cells. Moreover, the Dz enzymatic activity in the constrained structure can only be conditionally regulated by the specific intracellular mRNA sequences to silence the target gene with highly reduced side effects. Results show that the Apt/Dz catenane nanostructure can effectively inhibit the expression of the target gene and the proliferation of cancer cells with high specificity.

A fluorescent immunosensor for determination and imaging of circulating tumor cells based on a bifunctional DNA nanomachine

A fluorescent platform was developed for the determination and visualization of circulating tumor cells by a toehold-mediated bifunctional DNA nanomachine. In the presence of target tumor cells, the DNA nanomachine was activated. Multiple DNA products were formed, including dendritic DNA products and double-strand DNA products. Dendritic DNA products bound to their target cells for the visualization, while double-strand DNA products were released for the determination of tumor cells. At fluorescence excitation and emission wavelengths of 530 and 550 nm, this method could detect as low as 43 cells/mL (S/N = 3) with a linear range of 100 to 10,000 cells/mL. In clinical hydrothorax samples, this platform exhibited high reliability with a recovery of 93 to 116%. At the fluorescence excitation and emission wavelengths of 490 and 515 nm, the specificity and biocompatibility of this method were further verified by tumor cells imaging. Furthermore, the robustness of the toehold-mediated bifunctional DNA nanomachine was demonstrated by the specific gene mutation detection in single-cell analysis. Graphical abstract Schematic illustration of the fluorescent immunosensor for determination and imaging of circulating tumor cells. The method is based on aptamer-based recognition and toehold-mediated bifunctional DNA nanomachine.

Aptamer-tethered self-assembled FRET-flares for microRNA imaging in living cancer cells

We report an aptamer-tethered, self-assembled DNA nanowire as a multivalent vehicle for the intracellular delivery of FRET flares. The FRET flares are bound to the nanowire and fluorescently labeled donors and acceptors at two ends, respectively. In the absence of targets, the flares are captured by binding with the nanowires, separating the donor and acceptor (low FRET). However, in the presence of target miRNAs, the flares are displaced from the nanowire, subsequently forming hairpin structures that bring the donor and acceptor into close proximity (high FRET).

DNA branched junctions induced the enhanced fluorescence recovery of FAM-labeled probes on rGO for detecting Pb2

The reduced graphene oxide (rGO) could strongly adsorb and quench the fluorescence of dye-labeled single-stranded DNA (ssDNA); thus, it is widely applied in fluorescent sensors. However, these sensors may suffer from a limited sensitivity due to the low fluorescence recovery when adding the complementary DNA (cDNA) sequence. In this work, the powerful DNA branched junctions were constructed to improve the fluorescence recovery of FAM-labeled probe on rGO. In the presence of target Pb²⁺, the ribonucleotide (rA) in the substrate was cleaved specifically and the catalytic hairpin assembly of three metastable hairpins was further initiated, accompanied by the formation of DNA branched junctions. Then, the liberated Pb²⁺ could be recyclable. Impressively, the DNA branched junctions not only hybridize with the FAM-labeled probes with a high efficiency, but also are significantly undesirable for the rGO. Thus, a high fluorescence recovery of FAM-labeled probe on rGO was expected. The integration of the high fluorescence recovery and dual-cycle signal amplification endows the sensing strategy with a good performance for Pb²⁺ detection, including low detection limit (0.17 nM), good selectivity, and satisfactory practical applicability. The proposed DNA branched junctions offer a novel avenue to improve the fluorescence recovery of the dye-labeled probes on rGO for biological analysis.

Cascade signal amplification sensing strategy for highly specific and sensitive detection of homologous microRNAs in different molecular subtypes of breast cancer

Discriminative identification of homologous miRNAs in miRNA family with high specificity and sensitivity is crucial for accurate classification, diagnosis and prognosis of breast cancer. Herein, we report a reliable, sensitive, and selective assay by coupling fluorescence resonance energy transfer (FRET) with cascade signal amplification. The strategy is developed by designing two programmable DNA probes that can be triggered to shift from "off" to "on" state in a cascade hybridization reaction in the presence of target miRNA let-7a, leading to the generation of an amplified signal. The assay can detect concentrations as low as ∼3.0 pM let-7a and discriminate let-7a from other highly homologous members in the let-7 miRNA family. Moreover, it can also be used to determine let-7a levels at single-cell resolution and evaluate the drug efficacy of let-7a expression among various molecular types of breast cancer cell lines. The advantage of this assay is a combined result of signal generation and amplification triggered by target miRNA, which can satisfy an assay of analogous miRNA in a downregulated manner with high specificity. It has promising potential as a selective assay for homologous miRNAs in precision medicine.

Target-Induced Cascade Amplification for Homogeneous Virus Detection

Detection of viruses with high sensitivity is critical for the prevention and treatment of the related disease. Two homogeneous target-induced cascade amplification methods were proposed for the detection of enterovirus 71 and coxsackievirus B3. These methods both employ DNAzyme but differ in the way in which the DNAzyme is amplified. In the hybridization chain reaction (HCR)-based strategy, the DNAzyme is assembled by hairpin DNA strands, while in the rolling circle amplification (RCA)-based strategy, the DNAzyme is synthesized by the polymerase. On the basis of the virion structure, we investigated the effects of using only VP1-antibody or VP1-antibody and VP2-antibody on the detection. And the combination of two kinds of antibodies was found to further improve the performance of the detection. Subsequently, the simultaneous detection of EV71 and CVB3 was achieved by the RCA-based strategy. And the proposed methods were also applied in clinical samples analysis with a satisfactory result, showing great potential for applications in virus detection.

An Autonomous Nonenzymatic Concatenated DNA Circuit for Amplified Imaging of Intracellular ATP

A robust ATP aptasensor has been successfully constructed for intracellular imaging via the autonomous nonenzymatic cascaded hybridization chain reaction (Ca-HCR) circuit. This compact aptasensor is easily assembled by integrating the sensing module and amplification module, and is furtherly introduced for selective adenosine triphosphate (ATP) assay and for the sensitive tracking of varied ATP expressions in living cells. The ATP-targeting aptamer-encoded sensing module can specifically recognize ATP and release the initiator strand for successively motivating the two-layered HCR (hybridization chain reaction) circuit via the FRET transduction mechanism. The synergistic reaction acceleration of the two HCRs contributes to the high signal gain (amplification efficiency of N²). The whole reaction process was modeled and simulated by MATLAB to deeply explore the underlying molecular reaction mechanism, implying that the cascade HCR is sufficient enough to guarantee the ATP-recognition and amplification processes. The Ca-HCR-amplified aptasensor shows high sensitivity and selectivity for in vitro ATP assay, and can monitor these varied ATP expressions in living cells via intracellular imaging technique. Furthermore, the present aptasensor can be easily extended for monitoring other low-abundance biomarkers, which is especially important for precisely understanding these related biological processes.

Fluorometric determination of ssDNA based on functionalized magnetic microparticles and DNA supersandwich self-assemblies

A method is described for the determination of DNA via nucleic acid amplification by using nucleic acid concatemers that result from DNA supersandwich self-assemblies (SSAs). The method employs two auxiliary probes to form self-assembled biotin SSAs. These exhibit strong fluorescence if labeled with intercalator SYBR Green I. In the presence of the target (as exemplified for a 30-mer), streptavidin is released from the surface of the functionalized magnetic microparticles (FMMPs) by competitive hybridization on the surface. However, the SSA products do not conjugate to the FMMPs. This leads to a large amount of SYBR Green I intercalated into the concatemers and eventually results in amplified fluorescence in the supernate. The SSA products can be prepared beforehand, and amplification therefore can be completed within 50 min. The method is more efficient than any other conventional amplification. The detection limit for the 30-mer is 26.4 fM which is better by a factor of 10 compared to other amplification methods. Conceivably, the method can be further extended to the determination of a wide variety of targets simply by replacing the sequences of the probes. Finally, this rapid and highly sensitive method was employed for detection of Ebola virus gene (≈30-mer) and ATP in spiked serum with satisfactory results. Graphical abstract A high sensitivity and efficiency bioassay is described based on functionalized magnetic microparticles and DNA supersandwich self-assemblies.

Intracellular MicroRNA imaging using telomerase-catalyzed FRET ratioflares with signal amplification

Intracellular microRNA (miRNA) detection has attracted increasing attention, resulting in significant achievements. However, the development of an available tool that possesses a satisfactory signal-to-background ratio and high sensitivity for miRNA detection remains challenging. Herein, a class of telomerase-catalyzed FRET (fluorescence resonance energy transfer) ratioflares has been developed for the accurate sensing of low-abundance cancer-related miRNA both in a fluorescence assay and living cell imaging with signal amplification capacity. In this work, endogenous telomerase is led in a miRNA test system with signal amplification for the first time, wherein telomerase extends hexamer telomeric repeats (TTAGGG) using the 3' end of the capture probe as the primer. The synergetic work of telomerase and the catalyst strand (CS) makes the target miRNA circulate in the system, resulting in high sensitivity and an enhanced FRET signal an improved detection limit of 2.27 × 10-15 M. Meanwhile, telomerase-catalyzed FRET ratioflares allow the difference between cancer cells and normal cells to be increased reliably. Furthermore, low false positive signals resulting from chemical interference and minimized system fluctuations are achieved through ratiometric measurements.

Specific detection of RNA mutation at single-base resolution by coupling the isothermal exponential amplification reaction (EXPAR) with chimeric DNA probe-aided precise RNA disconnection at the mutation site

A chimeric DNA probe-aided RNase H-EXPAR approach is developed for the accurate and specific detection of RNA mutation at single-base resolution through a new site-specific RNase H cleavage mechanism.

Single-step multivalent capture assay for nucleic acid detection with dual-affinity regulation using mutation inhibition and allosteric activation

A single-step electrocatalytic biosensor with dual-affinity regulation enables a tunable dynamic range and tunable single nucleotide resolution for nucleic acid detection.

The rational modulation of receptor affinity through distal-site mutation and allosteric control is valuable in biosensor designing to tune the useful dynamic range. Our ability to programmatically engineer dual-affinity regulation into diverse affinities of target binding and activities of hybridization chain reaction, however, remains limited. By programmable engineering of the switching equilibria of the recognition hairpin using distal-site mutation inhibition and allosteric activation, we obtained a set of receptors varying significantly in affinities of target binding and activities of the hybridization chain reaction. For the first time, we developed an electrocatalytic biosensor for nucleic acid detection with a tunable dynamic range based on a conformational switch triggered bidirectional hybridization chain reaction and blocker assisted multivalent binding. This designable biosensor thus enables single-step incubation, diverse affinities of target binding, diverse efficiencies of signal amplification and diverse single nucleotide discrimination for quantitative analyses of nucleic acids of various lengths in serum, which holds great potential as a compelling platform suitable for liquid biopsy.