Bundling gold nanorods with RCA-produced DNA tape into an intelligently reconfigurable nanocluster bomb for multimodal precision cancer therapy

Via proposing an innovative assembly technique, we bundle cell-targeting aptamer-modified gold nanorods (AuNRs) with RCA product (RCA-p) tape into a reconfigurable nanocluster (ARGN) bomb for multimodal precision cancer therapy. Because each ARGN has 10 individual AuNRs, the short time of laser irradiation can make the temperature increase to 75 °C much higher than the lethal temperature of tumor cells, enabling the efficient photothermal therapy (PTT). Moreover, both siRNA-Plk1 (2820 per ARGN) and chemotherapeutic agents (15860 per ARGN) can be loaded into two specifically-designed containers in the internal cavity. Because the glomeroplasmatic structure enhances the resistance to enzymatic degradation, ARGN bomb can protect siRNAs from the digestion and avoid Dox leakage during in vivo circulation. Moreover, the spontaneous structural reorganization allows aptamers in the interior cavity move outward to the exterior surface, which magically offers the compensation of degraded aptamers and impair persistent in vivo cell targeting ability. The external stimuli (laser irradiation) promotes the release of chemotherapeutic agents and initiates the PTT/chemotherapy outcome, while endogenous stimuli (intracellular biomarkers) causes almost 100 % release of siRNA-Plk1 species and induces RNA interference therapy, completely inhibiting tumor growth without detectable off-target toxicity.

A dual-cycle DNA walker sensor for sensitive clinical detection of microRNAs

BACKGROUND

MicroRNAs (miRNAs) play crucial roles in both physiological and pathological processes, and are increasingly recognized as important biomarkers for cancers and other diseases. However, current detection methods for miRNA face challenges, including inadequate sensitivity and the need for temperature-controlled instruments, which hinder their clinical application. It is a pressing need for new strategies suitable for clinical miRNA detection.

RESULTS

We designed a dual-cycle DNA walker sensor (DDWS) by coupling duplex-specific nucleases enzyme-assisted signal amplification (DSNSA) with a DNA walker sensor. In the DSNSA process, the DSN enzyme specifically hydrolyzes DNA in DNA/target miRNA hybrid duplexes to facilitate the target cycling. The DNA walker sensor is activated by the trigger released from the DSNSA process, enabling a DNA walker cycle via the CHA reaction on magnetic microparticles (MMPs). The DDWS exhibited a strong linear relationship over a range of 600 fM to 600 nM and demonstrated excellent specificity for target miRNA. Furthermore, the DDWS was successfully applied to miRNA detection in real samples, including total RNAs extracted in cell samples and clinical papillary thyroid carcinoma (PTC) tissue samples.

SIGNIFICANCE

This DDWS assay holds great potential for evaluating miRNA expression levels across various biological matrices, contributing to the clinical diagnosis and prognosis of cancers.

Glucose Oxidase Coupling with Pistol-Like DNAzyme Based Colorimetric Assay for Sensitive Glucose Detection in Tears and Saliva

Non-invasive monitoring of glucose levels in tears and saliva is crucial for diagnosing and predicting various illnesses, such as diabetic nephropathy. However, the capability of the current glucose detection methods to identify small amounts of glucose with a high sensitivity remains a significant obstacle. This study proposes a simple, visual technique for sensitively detecting glucose levels from tears and saliva using glucose oxidase (GOx) to catalyze glucose and pistol-like DNAzyme (PLDz) to enhance the signal. In particular, the β-D-glucose present in the samples serves as the initial molecule that GOx identifies and catalyzes to generate gluconic acid and hydrogen peroxide (H2O2). The H2O2 induces the self-cleavage of PLDz, activating the "part b" sequence. This activation initiates catalytic hairpin assembly (CHA) and releases the DNAzyme section in the H1 probe. The DNAzyme acts as a peroxidase analog, facilitating the catalysis of the 3,3',5,5'-tetramethylbenzidine (TMB)-hydrogen peroxide (H2O2) system and resulting in color changes. The proposed method exhibits a broad detection range of six orders of magnitude and a low limit of 0.32 μM for glucose detection. Furthermore, the proposed method was highly effective in detecting glucose in saliva and tears, suggesting that it could potentially diagnose hyperglycemia-related disorders in clinical environments.

In situ imaging of intracellular miRNAs in tumour cells by branched hybridisation chain reaction

The ability to visualise microRNA in situ is crucial for studying microRNAs, their microRNA-associated biological functions and disease diagnosis. Traditional fluorescence in situ hybridisation methods based on paraformaldehyde fixation of microRNAs suffer from release of microRNAs from cells, which limits the sensitivity of in situ hybridisation, making them unsuitable for the detection of small, low-abundance microRNAs. To reduce the loss, microRNAs were covalently cross-linked to proteins within cells by combining EDC and paraformaldehyde, and the target microRNA was used as the initiator chain for a branched hybridisation chain reaction to detect microRNA expression levels in situ. A simplified branched hybridisation chain reaction can be realised by coupling two hybridisation chain reaction circuits with a hairpin linker. Upon forming the primary hybridisation chain reaction product with extended sequence, this sequence reacts with the linker hairpin H3 to release the initiator sequence, resulting in the formation of numerous dendritic branched hybridisation chain reaction products. Imaging results show that this technique can detect microRNAs with high sensitivity and selectivity at both the single-cell and single-molecule levels. Compared with the traditional fluorescence in situ hybridisation technique, this method greatly improves the sensitivity and image resolution of in situ imaging detection. Therefore, we believe that the target-initiated branched hybridisation chain reaction based in situ detection method provides a reliable assay platform for analysing disease-related microRNA expression.

Sensitivity-improved SERS detection of SARS-CoV-2 spike protein by Au NPs/COFs integrated with catalytic-hairpin-assembly amplification technology

BACKGROUND

The COVID-19 pandemic, caused by the novel coronavirus, has had a profound impact on global health and economies worldwide. This unprecedented crisis has affected individuals, communities, and nations in diverse manners. Developing simple and accurate diagnostic methods is an imperative task for frequent testing to mitigate the spread of the virus. Among these methods, SARS-CoV-2 antigen tests in clinical specimens have emerged as a promising diagnostic method for COVID-19 due to their sensitive and accurate detection of spike (S) protein, which plays a crucial role in viral infection initiation.

RESULTS

In this work, a dual-signal amplification surface enhanced Raman scattering (SERS)-based S protein biosensor was constructed based on Au NPs/COFs and enzyme-free catalytic hairpin assembly (CHA) amplification method. The approach relies on a released free DNA sequence (T), which is generated from the competition reaction between Aptamer/T and Aptamer/S protein, to trigger a CHA reaction. Due to the high binding affinity and selectivity between the S protein and its aptamer, CHA process was triggered with the maximum SERS tags (H2-conjugated Au@4-mercaptobenzonitrile@Ag) anchored onto Au NPs/COFs substrate surface. This SERS platform could detect the S protein at concentrations with high sensitivity (limit of detection = 3.0 × 10-16 g/mL), wide detection range (1 × 10-16 to 1 × 10-11 g/mL), acceptable reproducibility (relative standard deviation = 7.01 %) and excellent specificity. The biosensor was also employed to detect S protein in artificial human salivas.

SIGNIFICANCE

Thus, this study not only developed a novel Au NPs/COFs substrate exhibiting strong SERS enhancement ability and high reproducibility, but also proposed a promising dual-signal amplification SERS-based diagnostic method for COVID-19, holding immense potential for the detection of a wide range of antigens and infectious diseases in future applications.

Cyclic Multiple Primer Generation Rolling Circle Amplification Assisted Capillary Electrophoresis for Simultaneous and Ultrasensitive Detection of Multiple Pathogenic Bacteria

Efficient, accurate, and economical detection of pathogenic bacteria is crucial in ensuring food safety and preventing foodborne illnesses. How to fulfill the highly sensitive and simultaneous detection of multiple trace pathogenic bacteria is a big challenge. In this work, capillary electrophoresis coupled with a cyclic multiple primer generation rolling circle amplification (cyclic MPG-RCA) was studied for highly sensitive and simultaneous detection of three kinds of pathogenic bacteria. The cyclic MPG-RCA was based on a carefully designed clover-shaped DNA probe, in which three "leaves" corresponded to three types of aimed pathogenic bacteria: Shigella dysenteriae (S. dysenteriae), Salmonella enterica subsp. enterica serovar Typhi (S. Typhi), and Vibrio parahaemolyticus (V. parahaemolyticus). Under the optimal experimental conditions, the limits of detection (S/N = 3) of this method for bacterial target DNA were 11.4 amol·L-1 (S. dysenteriae), 4.88 amol·L-1 (S. Typhi), and 14.9 amol·L-1 (V. parahaemolyticus), and the conversion concentrations for the target bacteria were 10 colony-forming units (CFU)·mL-1 (S. dysenteriae), 3 CFU·mL-1 (S. Typhi), and 12 CFU·mL-1 (V. parahaemolyticus). This method had been applied to the detection of tap water samples with good results, which proved that it could be used as an effective tool for trace pathogenic bacteria monitoring in foods, environments, and medicines.

Combination of RCA and DNAzyme for Dual-Signal Isothermal Amplification of Exosome RNA

The RNA contained in exosomes plays a crucial role in information transfer between cells in various life activities. The accurate detection of low-abundance exosome RNA (exRNA) is of great significance for cell function studies and the early diagnosis of diseases. However, their intrinsic properties, such as their short length and high sequence homology, represent great challenges for exRNA detection. In this paper, we developed a dual-signal isothermal amplification method based on rolling circle amplification (RCA) coupled with DNAzyme (RCA-DNAzyme). The sensitive detection of low-abundance exRNA, the specific recognition of their targets and the amplification of the detection signal were studied and explored. By designing padlock probes to specifically bind to the target exRNA, while relying on the ligation reaction to enhance recognition, the precise targeting of exosome RNA was realized. The combination of RCA and DNAzyme could achieve a twice-as-large isothermal amplification of the signal compared to RCA alone. This RCA-DNAzyme assay could sensitively detect a target exRNA at a concentration as low as 527 fM and could effectively distinguish the target from other miRNA sequences. In addition, this technology was successfully proven to be effective for the quantitative detection of miR-21 by spike recovery, providing a new research approach for the accurate detection of low-abundance exRNA and the exploration of unknown exRNA functions.

Isothermal nucleic acid amplification technology in HIV detection

Nucleic acid testing for HIV plays an important role in the early diagnosis and monitoring of antiretroviral therapy outcomes in HIV patients and HIV-infected infants. Currently, the main molecular diagnostic methods employed are complex, time-consuming, and expensive to operate in resource-limited areas. Isothermal nucleic acid amplification technology overcomes some of the shortcomings of traditional assays and makes it possible to use point-of-care tests for molecular HIV detection. Here, we summarize and discuss the latest technological advances in isothermal nucleic acid amplification for HIV detection, with the intent of providing guidance for the development of subsequent HIV assays with high sensitivity and specificity.

A dual-amplification strategy-intergated SERS biosensor for ultrasensitive hepatocellular carcinoma-related telomerase activity detection

Telomerase has been considered as a biomarker for early diagnosis and prognosis assessment of hepatocellular carcinoma (HCC), while the highly sensitive and specific methods remain challenging. To detect telomerase, a novel surface-enhanced Raman scattering (SERS) biosensor was constructed using the dual DNA-catalyzed amplification strategy composed of strand displacement amplification (SDA) and catalytic hairpin assembly (CHA). This strategy relies on the extension reaction of telomerase primer induced by telomerase, forming long-stranded DNAs with repetitive sequence to catalyze the follow-up SDA event. Subsequently, the SDA products can trigger the CHA reaction between the SERS probes (Au-Ag nanocages (Au-AgNCs) modified with hairpin DNA1 and Raman reporters) and capture substrate (Au@SiO₂ array labeled with hairpin DNA2), resulting in the formation of numerous "hot spots" to significantly enhance the SERS signal. Results are promising that the established biosensor presented excellent reproducibility, specificity and sensitivity. Moreover, ELISA was applied as the golden standard to verify the application of the proposed biosensor in real samples and the results confirmed the satisfactory accuracy of our method. Therefore, the proposed SERS biosensor has the potential to be an ideal tool for the early screening of HCC.

Recent advances on the electrochemical and optical biosensing strategies for monitoring microRNA-21: a review

The small non-coding RNA, microRNA-21 (miR-21), is dysregulated in various cancers and can be considered an appropriate target for therapeutic approaches. Therefore, the detection of miR-21 concentration is important in the diagnosis of diseases. Low specificity and the cost of materials are two necessary limitations in the traditional diagnosis method such as RT-PCR, northern blotting and microarray analysis. Biosensor technology can play an effective role in improving the quality of human life due to its capacity of rapid diagnosis, monitoring different markers, suitable sensitivity, and specificity. Moreover, bioanalytical systems have an essential role in the detection of biomolecules or miRNAs due to their critical features, including easy usage, portability, low cost and real-time analysis. Electrochemical biosensors based on novel nanomaterials and oligonucleotides can hybridize with miR-21 in different ranges. Moreover, optical biosensors and piezoelectric devices have been developed for miR-21 detection. In this study, we have evaluated different materials used in bioanalytical systems for miR-21 detection as well as various nanomaterials that offer improved electrodes for its detection.

DNA walker-amplified signal-on electrochemical aptasensors for prostate-specific antigen coupling with two hairpin DNA probe-based hybridization reaction

Electrochemical aptasensing systems have been developed for screening low-abundance disease-related proteins, but most of them involve multiple washings and multi-step separation during measurements, and thus are disadvantageous for routine use. In this work, an innovative and simple electrochemical aptasensing platform was designed for the voltammetric detection of prostate-specific antigen (PSA) in biological fluids without any washing and separation steps. This system mainly included a PSA-specific aptamer, a DNA walker and two hairpin DNA probes (i.e., thiolated hairpin DNA1 and ferrocene-labeled hairpin DNA2). Introduction of target PSA caused the release of the DNA walker from a partially complementary aptamer/DNA walker hybridization strand. The dissociated DNA walker opened the immobilized hairpin DNA1 on the electrode, accompanying subsequent displacement reaction with hairpin DNA2, thus resulting in the DNA walker step-by-step reaction with numerous hairpin DNA1 probes on the sensing interface. In this case, numerous ferrocene molecules were close to the electrode to amplify the voltammetric signal within the applied potentials. All reactions and electrochemical measurements including the target/aptamer reaction and hybridization chain reaction were implemented in the same detection cell. Under optimal conditions, the fabricated electrochemical aptasensor gave good voltammetric responses relative to the PSA concentrations within the range of 0.001-10 ng mL^-1 at an ultralow detection limit of 0.67 pg mL^-1. A good reproducibility with batch-to-batch errors was acquired for target PSA down to 11.5%. Non-target analytes did not interfere with the voltammetric signals of the electrochemical aptasensors. Meanwhile, 15 human serum specimens were measured with electrochemical aptasensors, and displayed well-matched results in comparison with the referenced human PSA enzyme-linked immunosorbant assay (ELISA) method. Significantly, this method provides a new horizon for the quantitative monitoring of low-concentration biomarkers or nucleic acids.

Modern Methods for Assessment of microRNAs

The review discusses modern methods for the quantitative and semi-quantitative analysis of miRNAs, which are small non-coding RNAs affecting numerous biological processes such as development, differentiation, metabolism, and immune response. miRNAs are considered as promising biomarkers in the diagnosis of various diseases.

Selective and sensitive detection of miRNA-198 using single polymeric microfiber waveguide platform with heterogeneous CHA amplification strategy

Pancreatic cancer (PC), which has a high fatality rate, is a kind of cancer with poor diagnosis and poor prognosis. Development of selective and sensitive detection platform to diagnose and prognostic of PC has attracted considerable attention. The miRNA-198 has been reported a potential prognostic and early diagnostic marker signature of PC. Herein, we report a novel sensitive detection of miRNA-198 in buffer and serum based on one dimensional chitosan/fluorescein isothiocyanate (CS/FITC) fluorescent microfiber waveguide system combined with the catalytic hairpin assembly amplification strategy. By combination with condensing enrichment effect, the proposed detection platform exhibited high specificity and sensitivity to miRNA-198 target, giving a detection limit as low as 2 fM. More importantly, the proposed detection platform can be applied directly to distinguish the expression of miRNA-198 in clinical serum, affording the ability to distinguish pancreatic cancer patients from those of healthy human beings, and quantify the expression variation of miRNA-198 for the pancreatic cancer patients before and after resection, which may pave the way to develop novel clinical diagnostic equipment for cancer diagnosis and therapeutic evaluation.

Functional nucleic acid biosensors utilizing rolling circle amplification

Functional nucleic acids regulate rolling circle amplification to produce multiple detection outputs suitable for the development of point-of-care diagnostic devices.

Recent advances in catalytic hairpin assembly signal amplification-based sensing strategies for microRNA detection

Accumulative evidences have indicated that abnormal expression of microRNAs (miRNAs) is closely associated with many health disorders, making them be regarded as potentialbiomarkers for early clinical diagnosis. Therefore, it is extremely necessary to develop a highly sensitive, specific and reliable approach for miRNA analysis. Catalytic hairpin assembly (CHA) signal amplification is an enzyme-free toehold-mediated strand displacement method, exhibiting significant potential in improving the sensitivity of miRNA detection strategies. In this review, we first describe the potential of miRNAs as disease biomarkers and therapeutics, and summarize the latest advances in CHA signal amplification-based sensing strategies for miRNA monitoring. We describe the characteristics and mechanism of CHA signal amplification and classify the CHA-based miRNA sensing strategies into several categories based on the "signal conversion substance", including fluorophores, enzymes, nanomaterials, and nucleotide sequences. Sensing performance, limit of detection, merits and disadvantages of these miRNA sensing strategies are discussed. Moreover, the current challenges and prospects are also presented.

Proximity binding induced nucleic acid cascade amplification strategy for ultrasensitive homogeneous detection of PSA

In this work, based on the powerful cycle amplification cascades of proximity hybridization-induced hybridization chain reaction and catalyzed hairpin assembly, we engineered a nonenzymatic and ultrasensitive method which combined the Mg²⁺-DNAzyme recycling signal amplification for the analysis of the human prostate specific antigen. Herein, we adopted PSA-conjugates as triggers in the self-assembly process of two hairpin DNAs (H1, H2) into the products of the CHA which could activate the HCR to induce repeated hybridization. And both ends of each adjacent sequence of the HCR products could form a unit of Mg²⁺-DNAzyme which in presence of cofactor Mg²⁺ could recognize and cyclically cleave the hairpin probes in the solution and thus generate observably enhanced fluorescent signal. Benefit from the nucleic acid circuit amplification strategy, PSA of concentration low to 0.73 pg mL^-1 was detected in this system. This homogeneous sensing method in solution avoid the use of the sophisticated equipment and complex operation, as well as addition of artificial enzyme, thus greatly reducing the constraints and complexity of experimental conditions. Moreover, considering most protein biomarkers in serum don't have their corresponding aptamers, this sensing method provide a general sensing approach for homogeneous sensitive detection of these important protein biomarkers which transfer rough antigen-antibody interactivity to smart signal amplification sensing strategies, thus exhibiting a remarkable prospect in clinical application.

Recent applications of quantum dots in optical and electrochemical aptasensing detection of Lysozyme

Lysozyme (Lyz) is a naturally occurring enzyme that operates against Gram-positive bacteria and leads to cell death. This antimicrobial enzyme forms the part of the innate defense system of nearly all animals and exists in their somatic discharges such as milk, tears, saliva and urine. Increased Lyz level in serum is an important indication of several severe diseases and so, precise diagnosis of Lyz is an urgent need in biosensing assays. Up to know, various traditional and modern techniques have been introduced for Lyz determination. Although the traditional methods suffer from some significant limitations such as time-consuming, arduous, biochemical screening, bacterial colony isolation, selective enrichment and requiring sophisticated instrumentation or isotope labeling, some new modern approaches like aptamer-based biosensors (aptasensors) and quantum dot (QD) nanomaterials are the main goal in Lyz detection. Electrochemical and optical sensors have been highlighted because of their adaptability and capability to decrease the drawbacks of common methods. Using an aptamer-based biosensor, sensor selectivity is enhanced due to the specific recognition of the analyte. Thereby, in this review article, the recent advances and achievements in electrochemical and optical aptasensing detection of Lyz based on different QD nanomaterials and detection methods have been discussed in detail.

Light-Activated and Self-Driven Autonomous DNA Nanomachine Enabling Fluorescence Imaging of MicroRNA in Living Cells with Exceptional Precision and Efficiency

Owing to their favorable design flexibility and eminent signal amplification ability, DNA nanomachine-supported biosensors have provided an attractive avenue for intracellular fluorescence imaging, especially for DNA walkers. However, this promising option not only suffers from poor controllability but also needs to be supplied with additional driving forces on account of the frequent employment of metal ion-dependent DNAzymes. Aiming at overcoming these obstacles, we introduce some fruitful solutions. On one hand, innovative light-activated walking behavior induced by a photocleavage mode is established on the surfaces of gold nanoparticles, and such a photoselective sensing system can be perfectly prevented from pre-activating during the intracellular delivery process and made to achieve target identification only under irradiation using a moderate ultraviolet light source. On the other hand, this light-switchable sensing frame is encapsulated within a dissociable metal-organic framework (ZIF-8) to facilitate endocytosis and ensure sufficient internal cofactors (Zn²⁺) to realize a self-driven pattern in the acidic environment of the cell lysosome. Based on the abovementioned efforts, the newly constructed autonomous three-dimensional DNA walkers present satisfactory sensitivity (a limit of detection of down to 19.4 pM) and specificity (even distinguishing single-base changes) toward a model biomarker (microRNA-21). More importantly, the sensing method allows determination of the variations in targets in living cancer cells with exceptional precision and efficiency, offering a powerful assay platform for intracellular imaging.

Nucleic Acid Tests for Clinical Translation

Nucleic acids, including deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), are natural biopolymers composed of nucleotides that store, transmit, and express genetic information. Overexpressed or underexpressed as well as mutated nucleic acids have been implicated in many diseases. Therefore, nucleic acid tests (NATs) are extremely important. Inspired by intracellular DNA replication and RNA transcription, in vitro NATs have been extensively developed to improve the detection specificity, sensitivity, and simplicity. The principles of NATs can be in general classified into three categories: nucleic acid hybridization, thermal-cycle or isothermal amplification, and signal amplification. Driven by pressing needs in clinical diagnosis and prevention of infectious diseases, NATs have evolved to be a rapidly advancing field. During the past ten years, an explosive increase of research interest in both basic research and clinical translation has been witnessed. In this review, we aim to provide comprehensive coverage of the progress to analyze nucleic acids, use nucleic acids as recognition probes, construct detection devices based on nucleic acids, and utilize nucleic acids in clinical diagnosis and other important fields. We also discuss the new frontiers in the field and the challenges to be addressed.

MiRNA Detection Using a Rolling Circle Amplification and RNA-Cutting Allosteric Deoxyribozyme Dual Signal Amplification Strategy

A microRNA (miRNA) detection platform composed of a rolling circle amplification (RCA) system and an allosteric deoxyribozyme system is proposed, which can detect miRNA-21 rapidly and efficiently. Padlock probe hybridization with the target miRNA is achieved through complementary base pairing and the padlock probe forms a closed circular template under the action of ligase; this circular template results in RCA. In the presence of DNA polymerase, RCA proceeds and a long chain with numerous repeating units is formed. In the presence of single-stranded DNA (H1 and H2), multi-component nucleic acid enzymes (MNAzymes) are formed that have the ability to cleave substrates. Finally, substrates containing fluorescent and quenching groups and magnesium ions are added to the system to activate the MNAzyme and the substrate cleavage reaction, thus achieving fluorescence intensity amplification. The RCA-MNAzyme system has dual signal amplification and presents a sensing platform that demonstrates broad prospects in the analysis and detection of nucleic acids.

Padlock probe-based rolling circle amplification lateral flow assay for point-of-need nucleic acid detection

Sensitive, reliable and cost-effective detection of pathogens has wide ranging applications in clinical diagnostics and therapeutics, water and food safety, environmental monitoring, biosafety and epidemiology. Nucleic acid amplification tests (NAATs) such as PCR and isothermal amplification methods provide excellent analytical performance and significantly faster turnaround times than conventional culture-based methods. However, the inherent cost and complexity of NAATs limit their application in resource-limited settings and the developing world. To help address this urgent need, we have developed a sensitive method for nucleic acid analysis based on padlock probe rolling circle amplification (PLRCA), nuclease protection (NP) and lateral flow detection (LFA), referred to as PLAN-LFA, that can be used in resource-limited settings. The assay involves solution-phase hybridization of a padlock probe to target, sequence-specific ligation of the probe to form a circular template that undergoes isothermal rolling circle amplification in the presence of a polymerase and a labeled probe DNA. The RCA product is a long, linear concatenated single-stranded DNA that contains binding sites for the labeled probe. The sample is then exposed to a nuclease which selectively cleaves single-stranded DNA, the double-stranded labeled probe is protected from nuclease digestion and detected in a lateral flow immunoassay format to provide a visual, colorimetric readout of results. We have developed specific assays targeting beta-lactamase resistance gene for monitoring of antimicrobial resistance and Severe Acute Respiratory Syndrome-Coronavirus-2 (SARS-CoV-2, the novel coronavirus discovered in 2019) using the PLAN-LFA platform. The assay provides a limit of detection of 1.1 pM target DNA (or 1.3 × 106 copies per reaction). We also demonstrate the versatility and robustness of the method by performing analysis on DNA and RNA targets, and perform analysis in complex sample matrices like saliva, plant tissue extract and bacterial culture without any sample pretreatment steps.

A Cascade Signal Amplification Based on Dynamic DNA Nanodevices and CRISPR/Cas12a Trans-cleavage for Highly Sensitive MicroRNA Sensing

The variations of microRNA (miRNA) expression can be valuable biomarkers in disease diagnosis and prognosis. However, current miRNA detection techniques mainly rely on reverse transcription and template replication, which suffer from slowness, contamination risk, and sample loss. To address these limitations, here we introduce a cascade toehold-mediated strand displacement reaction (CTSDR) and CRISPR/Cas12a trans-cleavage for highly sensitive fluorescent miRNA sensing, namely CTSDR-Cas12a. In this work, the target miRNA hybridizes with the terminal toehold site of a rationally designed probe and subsequently initiates dynamic CTSDR, leading to enzyme-free target recycling and the production of multiple programmable DNA duplexes. The obtained DNA duplex acts as an activator to trigger Cas12a trans-cleavage, generating significantly amplified fluorescence readout for highly sensitive detection of the miRNA target. Under the optimal conditions, the developed sensing method can detect target miRNA down to 70.28 fM with a wide linear range from 100 fM to 100 pM. In particular, by designing a set of probes and crRNAs, we demonstrate its broad applicability for the detection of six kinds of miRNAs with high sequence specificity. Furthermore, the method can be satisfactorily applied to monitor miR-21 in total RNA extracted from cells and clinical serum samples. Considering the high sensitivity, specificity, universality, and ease of handling, this strategy provides a great potential platform for the detection of miRNA biomarkers in molecular diagnostic practice.

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.

Rolling Circle Replication for Biosensing, Bioimaging, and Biomedicine

Rolling circle replication (RCR), including rolling circle amplification (RCA) and rolling circle transcription (RCT), is an isothermal enzymatic reaction. Because of its high amplification efficiency, RCR is a powerful biosensing tool for detecting biomolecules. In recent years, RCR has also been extended to the field of bioimaging to better understand biological pathways. Furthermore, RCR provides a simple technique to design and generate DNA/RNA structures with unique advantages in delivering drugs and enhanced targeting ability. In this review, we introduce the fundamentals of RCR and describe the most recent advances in RCR-based detection methods and delivery vehicles for biosensing, bioimaging, and biomedicine. Finally, some challenges and further opportunities of RCR-based biotechnology are discussed.

Reverse transcription lesion-induced DNA amplification: An instrument-free isothermal method to detect RNA

One challenge in point-of-care (POC) diagnostics is the lack of room-temperature methods for RNA detection based on enzymatic amplification and visualization steps. Here we perform reverse transcription lesion-induced DNA amplification (RT-LIDA), an isothermal amplification method that only requires T4 DNA ligase. RT-LIDA involves the RNA-templated ligation of DNA primers to form complementary DNA (cDNA) followed by toehold-mediated strand displacement of the cDNA and its exponential amplification via our isothermal ligase chain reaction LIDA. Each step is tuned to proceed at 28 °C, which falls within the range of global room temperatures. Using RT-LIDA, we can detect as little as ∼100 amol target RNA and can distinguish RNA target from total cellular RNA. Finally, we demonstrate that the resulting DNA amplicons can be detected colorimetrically, also at room temperature, by rapid, target-triggered disassembly of DNA-modified gold nanoparticles. This integrated amplification/detection platform requires no heating or visualization instrumentation, which is an important step towards realizing instrument-free POC testing.

Recent advances in rolling circle amplification-based biosensing strategies-A review

Rolling circle amplification (RCA) is an efficient enzymatic isothermal reaction that using circular probe as a template to generate long tandem single-stranded DNA or RNA products under the initiation of short DNA or RNA primers. As a simplified derivative of natural rolling circle replication which synthesizes copies of circular nucleic acids molecules such as plasmids, RCA amplifies the circular template rapidly without thermal cycling and finds various applications in molecular biology. Compared with other amplification strategies, RCA has many obvious advantages. Firstly, because of the strict complementarity required in ligation of a padlock probe, it endows the RCA reaction with high specificity and can even be utilized to distinguish single base mismatches. Secondly, through the introduction of multiple primers, exponential amplification can be achieved easily and leads to a good sensitivity. Thirdly, RCA products can be customized by manipulating circular templates to generate functional nucleic acids such as aptamer, DNAzymes and restriction enzyme sites. Moreover, the RCA has good biocompatibility and is especially suitable for in situ detection. Therefore, RCA has attracted considerable attention as an efficient and potential tool for highly sensitive detection of biomarkers. Herein, we comprehensively introduce the fundamental principles of RCA technology, summarize it from three aspects including initiation mode, amplification mode and signal output mode, and discuss the recent application of RCA-based biosensor in this review.

Autocatalytic DNAzyme assembly for amplified intracellular imaging

The autocatalytic HCR-DNAzyme platform was constructed as a versatile amplification platform for intracellular microRNA imaging by integrating hybridization chain reaction (HCR) circuit with DNAzyme biocatalysis. The HCR-assembled multifunctional DNAzyme nanowires produce new HCR triggers and numerous transducer DNAzyme amplifier, and thus shows great promise in earlier cancer diagnosis.

Enzyme-Assisted Nucleic Acid Detection for Infectious Disease Diagnostics: Moving toward the Point-of-Care

Driven by complex and interconnected factors, including population growth, climate change, and geopolitics, infectious diseases represent one of the greatest healthcare challenges of the 21st century. Diagnostic technologies are the first line of defense in the fight against infectious disease, providing critical information to inform epidemiological models, track diseases, decide treatment choices, and ultimately prevent epidemics. The diagnosis of infectious disease at the genomic level using nucleic acid disease biomarkers has proven to be the most effective approach to date. Such methods rely heavily on enzymes to specifically amplify or detect nucleic acids in complex samples, and significant effort has been exerted to harness the power of enzymes for in vitro nucleic acid diagnostics. Unfortunately, significant challenges limit the potential of enzyme-assisted nucleic acid diagnostics, particularly when translating diagnostic technologies from the lab toward the point-of-use or point-of-care. Herein, we discuss the current state of the field and highlight cross-disciplinary efforts to solve the challenges associated with the successful deployment of this important class of diagnostics at or near the point-of-care.

An enzyme-free electrochemical biosensor based on target-catalytic hairpin assembly and Pd@UiO-66 for the ultrasensitive detection of microRNA-21

MicroRNA-21 (miR-21) has been widely investigated as important biomarkers for cancer diagnosis and treatment. Herein, a highly sensitive nonenzymatic electrochemical biosensor based on Pd@metal-organic frameworks (Pd@UiO-66) and target-catalytic hairpin assembly (CHA) with target recycling approach has been proposed for the detection of miR-21. The proposed biosensor integrates the efficient CHA strategy and excellent electrocatalytic performance of Pd@UiO-66 nanocomposites. The concentration of miRNA-21 is related to the amount of the adsorbed electrocatalyst, leading to the different electrochemical signals for readout towards paracetamol (AP). This biosensor shows a low limit of detection of 0.713 fM with the dynamic range of 20 fM -600 pM under the optimal experimental conditions, providing a powerful platform for detecting miR-21. Furthermore, the designed biochemical self-assembly strategy of this electrochemical biosensor is promising candidate for potential applications in the analysis of other important genetic biomarkers for early diagnosis of cancers.

Electrochemical biosensor for miRNA-21 based on gold-platinum bimetallic nanoparticles coated 3-aminopropyltriethoxy silane

We report an electrochemical biosensor based on gold platinum bimetallic nanoparticles (AuPtBNPs)/3-aminopropyltriethoxy silane (APTS) nanocomposite coated fluorine-doped tin oxide (FTO) as a biosensing platform for hybridization-based detection of miRNA-21. Field Emission-Scanning Electron Microscopy (FE-SEM), Fourier Transform Infrared Spectroscopy (FT-IR) and electrochemical measurements were carried out to ensure the successful construction of the biosensor. The amount of cDNA immobilized on electrode surface and hybridization time required for the miRNA-21 sensing were optimized. The biosensing platform showed detection limit of 0.63 fM with wide linear range i.e. 1 fM-100 nM for miRNA-21 detection. The biosensing strategy demonstrates a good recovery yield from 90.18% to 94.6% in serum samples. It offers good selectivity for its complementary miRNA compared to the non-complementary miRNAs. Other analytical features of the biosensor such as stability, reusability and reproducibility were also tested, providing appropriate results.

DNAzyme-Based Target-Triggered Rolling-Circle Amplification for High Sensitivity Detection of microRNAs

MicroRNAs regulate and control the growth and development of cells and can play the role of oncogenes and tumor suppressor genes, which are involved in the occurrence and development of cancers. In this study, DNA fragments obtained by target-induced rolling-circle amplification were constructed to complement with self-cleaving deoxyribozyme (DNAzyme) and release fluorescence biomolecules. This sensing approach can affect multiple signal amplification permitting fluorescence detection of microRNAs at the pmol L⁻¹ level hence affording a simple, highly sensitive, and selective low cost detection platform.

An anchored monopodial DNA walker triggered by proximity hybridization for amplified amperometric biosensing of nucleic acid and protein

This work designed an anchored monopodial DNA walker to amplify amperometric biosensing signal for sensitive detection of nucleic acid and protein. The biosensing surface was constructed by self-assembling hairpin DNA1 (H1) and small amount of P1-W (probe DNA1 hybridized with walking DNA) on a gold electrode. In the presence of target molecule, the walker could be triggered by the surface proximity hybridization product of P1, target and P2 to induce the cyclic hybridization of H1 with ferrocene modified hairpin DNA2 (H2-Fc), which took electroactive Fc to the electrode surface for amplified amperometric detection of the target. By linking P1 and P2 with dual specific DNA strands, aptamers or antibodies to recognize the target for proximity hybridization of P1 and P2, the walker amplified amperometric strategy could be used for highly sensitive biosensing of different targets. Using DNA and thrombin as the target models, the proposed biosensing methods achieved the linear range from 0.2 pM to 2 nM with a detection limit of 0.11 pM and 1.0 pM to 10 nM with a detection limit of 0.61 pM, respectively. The specific recognition process endowed the strategy with high selectivity and potential applications.

Homogeneous multiplexed digital detection of microRNA with ligation-rolling circle amplification

MicroRNA was transformed into a DNA nanoflower ball by LRCA reaction for homogeneous multiplexed digital detection using flow cytometry.

Polymerization-driven successive collapse of DNA dominoes enabling highly sensitive cancer gene diagnosis

We propose a novel fluorescence assay method by designing a polymerization-driven DNA dominoes collapse (PDDC) strategy, enabling highly sensitive detection of p53 gene (as a model analyte) and single nucleotide polymorphism analysis.

Catalytic hairpin assembly-based double-end DNAzyme cascade-feedback amplification for sensitive fluorescence detection of HIV-1 DNA

In this work, a simple all-nucleic acid cascade-feedback amplification strategy for homogeneous and protein enzyme-free fluorescence detection of HIV-1 related DNA (HIV-1 DNA) has been proposed by integrating catalytic hairpin assembly (CHA) circuit with double-end Mg²⁺-dependent DNAzyme autocatalytic feedback amplification. Here, the active double-end DNAzyme assemblies were derived from target-catalyzed CHA circuit, which further circularly cleaved the ribonucleotide-containing quenched fluorogenic hairpin substrates to generate distinctly amplified fluorescence signal. Meanwhile, the released quencher-labeled fragments as target DNA analogues were also able to autocatalyze CHA-DNAzyme reaction process, thus improving the determination sensitivity of HIV-1 DNA. The result demonstrated that the fluorescence intensity increment of double-end DNAzyme was over 3 times higher than that of single-end DNAzyme. The sensing method displayed a good linear range from 1 pM to 2 nM with a detectable minimum concentration of 1 pM and high specificity towards different mismatched target DNAs. Moreover, the practical application potential of the proposed method for target DNA detection in complex biological matrices was also assessed. Considering the appealing feature of programmable nucleic acids in CHA-DNAzyme sensing platform, the current strategy may provide a prospective design for detection of broad-spectrum nucleic acid biomarkers.

Highly Sensitive in Vitro Diagnostic System of Pandemic Influenza A (H1N1) Virus Infection with Specific MicroRNA as a Biomarker

Several microRNAs (miRNAs) have been reported to be closely related to influenza A virus infection, replication, and immune response. Therefore, the development of the infectious-disease detection system using miRNAs as biomarkers is actively underway. Herein, we identified two miRNAs (miR-181c-5p and miR-1254) as biomarkers for detection of pandemic influenza A H1N1 virus infection and proposed the catalytic hairpin assembly-based in vitro diagnostic (CIVD) system for a highly sensitive diagnosis; this system is composed of two sets of cascade hairpin probes enabling to detect miR-181c-5p and miR-1254. We demonstrated that CIVD kits could not only detect subnanomolar levels of target miRNAs but also distinguish even single-base mismatches. Moreover, this CIVD kit has shown excellent detection performance in real intracellular RNA samples and confirmed results similar to those of conventional methods (microarray and quantitative real-time polymerase chain reaction).

Fluorometric determination of microRNA by using an entropy-driven three-dimensional DNA walking machine based on a catalytic hairpin assembly reaction on polystyrene microspheres

An entropy-driven 3-D DNA walking machine is presented which involves catalytic hairpin assembly (CHA) for detection of microRNA. A 3-D DNA walking machine was designed that uses streptavidin-coated polystyrene microspheres as track carriers to obtain reproducibility. The method was applied to microRNA 21 as a model analyte. Continuous walking on the DNA tracks is achieved via entropy increase. This results in a disassembly of ternary DNA substrates on polystyrene microspheres and leads to cycling of microRNA 21. The release of massive auxiliary strands from ternary DNA substrates induces the CHA. This is accompanied by in increase in fluorescence, best measured at excitation/emission wavelengths of 480/520 nm. On account of entropy-driven reaction, the assay is remarkably selective. It can differentiate microRNA 21 from homologous microRNAs in giving a signal that is less than 5% of the signal for microRNA 21 except for microRNA-200b. The assay works in the 50 pM to 20 nM concentration range and has a 41 pM detection limit. The method displays good reproducibility (between 1.1 and 4.2%) and recovery (from 99.8 to 104.0%). Graphical abstract An entropy-driven 3-D DNA walking machine is described. It is based on the use of polystyrene microspheres and of a catalytic hairpin assembly reaction for sensitive microRNA detection. Figure Notes: AS represents auxiliary strand; S represents substrate strand; LS represents link strand; F represents fuel nucleic acid; RepF represents nucleic acid labeled with FAM; RepQ represents nucleic acid labeled with BHQ1.