Tetrahedral DNA probe coupling with hybridization chain reaction for competitive thrombin aptasensor

Synthesis of dual models multivalent activatable aptamers based on HCR and RCA for ultrasensitive detection of Salmonella typhimurium

Aptamers have superior structural properties and have been widely used in bacterial detection methods. However, the problem of low affinity still exists in complex sample detection. In contrast, hybridization chain reaction (HCR)-based model I and rolling circle amplification (RCA)-based model II multivalent activatable aptamers (multi-Apts) can fulfill the need for low-cost, rapid, highly sensitive and high affinity detection of S. typhimurium. In our research, two models of multi-Apts were designed. First, a monovalent activatable aptamer (mono-Apt) was constructed by fluorescence resonance energy transfer (FRET) with an S. typhimurium aptamer and its complementary chain of BHQ1. Next, the DNA scaffold was obtained by HCR and RCA, and the multi-Apts were obtained by self-assembly of the mono-Apt with a DNA scaffold. In model I, when target was presented, the complementary chain BHQ1 was released due to the binding of multi-Apts to the target and was subsequently adsorbed by UIO66. Finally, a FRET-based fluorescence detection signal was obtained. In mode II, the multi-Apts bound to the target, and the complementary chain BHQ1 was released to become the trigger chain for the next round of amplification of HCR with a fluorescence detection signal. HCR and RCA based multi-Apts were able to detect S. typhimurium as low as 2 CFU mL-1 and 1 CFU mL-1 respectively. Multi-Apts amplification strategy provides a new method for early diagnosis of pathogenic microorganisms in foods.

An electrochemical biosensor for the amplification of thrombin activity by perylene-mediated photoinitiated polymerization

BACKGROUND

Thrombin, a coagulation system protease, is a key enzyme involved in the coagulation cascade and has been developed as a marker for coagulation disorders. However, the methods developed in recent years have the disadvantages of complex operation, long reaction time, low specificity and sensitivity. Meanwhile, thrombin is at a lower level in the pre-disease period. Therefore, to accurately diagnose the disease, it is necessary to develop a fast, simple, highly sensitive and specific method using signal amplification technology.

RESULTS

We designed an electrochemical biosensor based on photocatalytic atom transfer radical polymerization (photo-ATRP) signal amplification for the detection of thrombin. Sulfhydryl substrate peptides (without carboxyl groups) are self-assembled to the gold electrode surface via Au-S bond and serve as thrombin recognition probes. The substrate peptide is cleaved in the presence of thrombin to generate -COOH, which can form a carboxylate-Zr(IV)-carboxylate complex via Zr(IV) and initiator (α-bromophenylacetic acid, BPAA). Subsequently, an electrochemical biosensor was prepared by introducing polymer chains with electrochemical signaling molecules (ferrocene, Fc) onto the electrode surface by photocatalytic (perylene, Py) mediated ATRP using ferrocenylmethyl methacrylate (FMMA) as a monomer. The concentration of thrombin was evaluated by the voltammetric signal generated by square wave voltammetry (SWV), and the result showed that the biosensor was linear between 1.0 ng/mL ∼ 10 fg/mL, with a lower detection limit of 4.0 fg/mL (∼0.1 fM). Moreover, it was shown to be highly selective for thrombin activity in complex serum samples and for thrombin inhibition screening.

SIGNIFICANCE

The biosensor is an environmentally friendly and economically efficient strategy while maintaining the advantages of high sensitivity, anti-interference, good stability and simplicity of operation, which has great potential for application in the analysis of complex samples.

An off-on fluorescence aptasensor for trace thrombin detection based on FRET between CdS QDs and AuNPs

An off-on fluorescence aptasensor was developed for trace thrombin detection based on fluorescence resonance energy transfer (FRET) between CdS QDs and gold nanoparticles (AuNPs). Using DNA pairwise hybridization of the aptamer to the complementary DNA (cDNA), the CdS QDs (energy donor) were tightly coupled to the AuNPs (energy acceptor), resulting in the occurrence of FRET and there was a dramatic fluorescence quenching of CdS QDs (turn off). When the thrombin was added to the fluorescence aptasensor, the specific binding of the aptamer to the target formed a G-quadruplex that caused the AuNPs receptor to detach and the DNA duplex to be disassembled. The process would inhibit the FRET which contribute to the recovery of fluorescence (turn on) and an "off-on" fluorescence aptasensor for thrombin detection was constructed accordingly. Under optimal conditions, the fluorescence recovery showed good linearity with the concentration of thrombin in the range of 1.35-54.0 nmol L-1, and the detection limit was 0.38 nmol L-1 (S/N = 3, n = 9). Importantly, the fluorescence aptasensor presented excellent specificity for thrombin, and was successfully applied to the quantitative determination of thrombin in real serum with satisfactory recoveries of 98.60-102.2%.

Recent Progresses in Development of Biosensors for Thrombin Detection

Thrombin is a serine protease with an essential role in homeostasis and blood coagulation. During vascular injuries, thrombin is generated from prothrombin, a plasma protein, to polymerize fibrinogen molecules into fibrin filaments. Moreover, thrombin is a potent stimulant for platelet activation, which causes blood clots to prevent bleeding. The rapid and sensitive detection of thrombin is important in biological analysis and clinical diagnosis. Hence, various biosensors for thrombin measurement have been developed. Biosensors are devices that produce a quantifiable signal from biological interactions in proportion to the concentration of a target analyte. An aptasensor is a biosensor in which a DNA or RNA aptamer has been used as a biological recognition element and can identify target molecules with a high degree of sensitivity and affinity. Designed biosensors could provide effective methods for the highly selective and specific detection of thrombin. This review has attempted to provide an update of the various biosensors proposed in the literature, which have been designed for thrombin detection. According to their various transducers, the constructions and compositions, the performance, benefits, and restrictions of each are summarized and compared.

Electrochemical aptasensor based on Ce3NbO7/CeO2@Au hollow nanospheres by using Nb.BbvCI-triggered and bipedal DNA walker amplification strategy for zearalenone detection

Herein, an electrochemical aptasensor combining Nb.BbvCI-triggered bipedal DNA walking strategy was constructed for ultrasensitive assay of zearalenone (ZEN). The aptasensor used Ce₃NbO₇/CeO₂ @Au hollow nanospheres as electrode modification material and PdNi@MnO₂/MB as the signal label. Importantly, the Ce₃NbO₇/CeO₂ synthesized by hydrothermal method were combined with Au nanoparticles and applied to the electrode surface. The as-prepared Ce₃NbO₇/CeO₂ @Au possessed a large surface area, excellent electrical conductivity, stability and more binding sites. PdNi@MnO₂ with high specific surface area and porosity combined with molecule methylene blue (MB) was introduced into electrodes as the signal label. The proposed aptasensor utilized the advantages of specific recognition of aptamers and target molecules to release bipedal DNA walker (w-DNA), and then the w-DNA was triggered by Nb.BbvCI and entered the cycle to release more signal probes. The feasibility of this strategy was recorded by the differential pulse voltammetry (DPV) method. Under the optimized conditions, the electrochemical aptasensor exhibited a wide linear dynamic range from 1 × 10^-4 to 1 × 10³ ng mL^-1 with a low detection limit of 4.57 × 10^-6 ng mL^-1. Moreover, the aptasensor had high selectivity, good stability, excellent repeatability and provided an effective method for the trace detection of ZEN in real samples.

Sensitive and selective detection of Mucin1 in pancreatic cancer using hybridization chain reaction with the assistance of Fe3O4@polydopamine nanocomposites

Pancreatic cancer is characterized as the worst for diagnosis lacking symptoms at the early stage, which results in a low overall survival rate. The frequently used techniques for pancreatic cancer diagnosis rely on imaging and biopsy, which have limitations in requiring experienced personnel to operate the expensive instruments and analyze the results. Therefore, there is a high demand to develop alternative tools or methods to detect pancreatic cancer. Herein, we propose a new strategy to enhance the detection sensitivity of pancreatic cancer cells both in biofluids and on tissues by combining the unique property of dopamine coated Fe3O4 nanoparticles (Fe3O4@DOP NPs) to specifically quench and separate free 6-carboxyfluorescein (FAM) labeled DNA (H1-FAM/H2-FAM), and the key feature of hybridization chain reaction (HCR) amplification. We have determined the limit of detection (LOD) to be 21 ~ 41 cells/mL for three different pancreatic cancer cell lines. It was also discovered that the fluorescence intensity of pancreatic cancer cells was significantly higher than that of HPDE-C7 and HepG-2 cells (control cell lines), which express lower MUC1 protein. Moreover, the HCR amplification system was used to identify the cancer cells on pancreatic tissue, which indicated the versatility of our strategy in clinical application. Therefore, the presented detection strategy shows good sensitivity, specificity and has great potential for the diagnosis of pancreatic cancer.

Graphene oxide nanosheet-mediated fluorescent RPA "turn-on" biosensor for rapid RNAi transgenic plant detection

In this paper preliminarily verified that graphene oxide (GO) nanomaterials enhanced the recombinase polymerase amplification (RPA). GO nanosheets improved the efficiency of RPA amplification by absorbing ingredients to induce local aggregation. The recombinase initially aggregated with the primers to form nucleoprotein filaments, absorbed on the GO nanosheets, changing the structure. Therefore, an isothermal fluorescence biosensor was developed based on GO nanosheets enhanced the RPA to detect RNA interference (RNAi) transgenic plants. FAM-labeled primers were absorbed and quenched by the GO nanosheets. After amplification, the primers were extended into double-stranded DNA, detaching from the GO surface to recover the fluorescent signal. The biosensor displayed high sensitivity and selectivity and showed an excellent relationship ranging from 1.5 to 100 ng of genome DNA, with a detection limit (LOD) of 1.5 ng. Consequently, the biosensor provides an enhanced isothermal method for detecting genetically modified (GM) products and exhibits significant potential for molecular detection.

High-Sensitivity Fluorescence Detection for lung cancer CYFRA21-1 DNA based on Accumulative Hybridization of Quantum Dots

Sensitive detection of circulating tumor DNA (ctDNA) in vitro has attracted growing attention owing to its potential application in diagnostics of cancer. In this study, we synthesized hydrophilic AgInS2@ZnS core-shell...

Exponential Increase in an Ionic Signal: A Dominant Role of the Space Charge Effect on the Outer Surface of Nanochannels

Nanochannels have advantage in sensitive analyses due to the confinement effects on ionic signal in nano- or sub-nanometric confines but could realize further gains by optimizing signal mechanism. Making target recognitions on the outer surface of nanochannels has been verified to improve target recognitions and signal conversions by maximizing surfaces accessible to targets and ions, but until recently, the signal mechanism has been still unclear. Using electroneutral peptide nucleic acid (PNA) and negative-charged DNA, we verified a dominant space charge effect on an ionic signal on the outer surface of nanochannels. A typical exponential increase of the ionic signal with the charge density on the outer surface has been demonstrated through the PNA-PNA, PNA-DNA, DNA-DNA hybrid, DNA cleavage, and hybridization chain reaction. These results challenge the essential role of steric hindrance on the ionic signal and describe a new ion passageway surrounded and accelerated by the stern layer of charged species on the nanochannel outer surface.

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.

Specific and sensitive detection of CircRNA based on netlike hybridization chain reaction

Circular RNA (circRNA), as a new class of biomarker, plays an important role in the occurrence and development of cancer. However, the limitations of detection methods in recent years have severely restricted the related research of circRNA. Here, we have developed an effective circRNA detection method based on the thermostatic netlike hybridization chain reaction (HCR). It combines reverse transcription-rolling circle amplification (RT-RCA) with well-designed netlike HCR to achieve dual selection and dual signal amplification, which can eliminate the interference of linear isomers. This two-dimensional netlike HCR is composed of an ingeniously designed trigger chain and two hairpin fuel probes, which can generate a stable network structure with RT-RCA products containing multiple sets of repeats at a constant temperature, thereby producing enhanced fluorescent signals. Systematic studies reveal that the optimized netlike HCR system has higher detection efficiency for DNA strands containing multiple sets of repetitive sequences, can detect circRNA as low as 0.1 pM, and has excellent selectivity. By using human tumor cell lines and tissues, it has been verified that the netlike HCR-based method can accurately detect specific circRNA in real biological samples without RNase R enrichment, which provides a simple and useful platform for detecting low-abundance circRNA. Furthermore, the proposed strategy is also a potential method for detecting some genes containing repetitive sequences, such as telomere DNA, centromere DNA and ribosomal DNA (rDNA).

DNA Based and Stimuli-Responsive Smart Nanocarrier for Diagnosis and Treatment of Cancer: Applications and Challenges

The rapid development of multidrug co-delivery and nano-medicines has made spontaneous progress in tumor treatment and diagnosis. DNA is a unique biological molecule that can be tailored and molded into various nanostructures. The addition of ligands or stimuli-responsive elements enables DNA nanostructures to mediate highly targeted drug delivery to the cancer cells. Smart DNA nanostructures, owing to their various shapes, sizes, geometry, sequences, and characteristics, have various modes of cellular internalization and final disposition. On the other hand, functionalized DNA nanocarriers have specific receptor-mediated uptake, and most of these ligand anchored nanostructures able to escape lysosomal degradation. DNA-based and stimuli responsive nano-carrier systems are the latest advancement in cancer targeting. The data exploration from various studies demonstrated that the DNA nanostructure and stimuli responsive drug delivery systems are perfect tools to overcome the problems existing in the cancer treatment including toxicity and compromised drug efficacy. In this light, the review summarized the insights about various types of DNA nanostructures and stimuli responsive nanocarrier systems applications for diagnosis and treatment of cancer.

Hybridization chain reaction and its applications in biosensing

To pursue the sensitive and efficient detection of informative biomolecules for bioanalysis and disease diagnosis, a series of signal amplification techniques have been put forward. Among them, hybridization chain reaction (HCR) is an isothermal and enzyme-free process where the cascade reaction of hybridization events is initiated by a target analyte, yielding a long nicked dsDNA molecule analogous to alternating copolymers. Compared with conventional polymerase chain reaction (PCR) that can proceed only with the aid of polymerases and complicated thermal cycling, HCR has attracted increasing attention because it can occur under mild conditions without using enzymes. As a powerful signal amplification tool, HCR has been employed to construct various simple, sensitive and economic biosensors for detecting nucleic acids, small molecules, cells, and proteins. Moreover, HCR has also been applied to assemble complex nanostructures, some of which even act as the carriers to execute the targeted delivery of anticancer drugs. Recently, HCR has engendered tremendous progress in RNA imaging applications, which can not only achieve endogenous RNA imaging in living cells or even living animals but also implement imaging-guided photodynamic therapy, paving a promising path to promote the development of theranostics. In this review, we begin with the fundamentals of HCR and then focus on summarizing the recent advances in HCR-based biosensors for biosensing and RNA imaging strategies. Further, the challenges and future perspective of HCR-based signal amplification in biosensing and theranostic application are discussed.

A competitive colorimetric aptasensor transduced by hybridization chain reaction-facilitated catalysis of AuNPs nanozyme for highly sensitive detection of saxitoxin

Saxitoxin (STX) is a small molecule toxin (Mw. ca. 299 g/mol) with high acute toxicity, and it has urgent need of facile analytical methods. Herein, a competitive colorimetric aptasensor was developed for highly sensitive detection of STX. An anti-STX aptamer was hybridized with a complementary strand on the magnetic beads and was competitively bound by STX. The supernatant containing the aptamer binding to STX was obtained by magnetic separation, which could trigger hybridization chain reaction (HCR) to generate rigid double stranded DNAs (dsDNAs) with sticky end and variable length. These HCR-dsDNAs were found to be able to facilitate significant enhancement on the peroxidase-like catalytic capability of AuNPs nanozyme towards 3,3,5,5-tetramethylbenzidine (TMB). The concentration of STX was responded in a "turn on" mode, based on the amplified colorimetric transduction thereof. The aptasensor realized high sensitivity, with a limit of detection (LOD) as low as 42.46 pM. Moreover, a wide linear detection range of 78.13-2500 pM, good selectivity, as well as good recovery rates of 106.2-113.5% when analyzing STX in real shellfish samples were obtained. This strategy could be referred to develop robust aptasensors for simple and highly sensitive detection of other small molecules and toxins.

A novel chemiluminescence imaging immunosensor for prostate specific antigen detection based on a multiple signal amplification strategy

A novel chemiluminescence (CL) imaging platform was constructed for prostate specific antigen (PSA) detection in a multiple signal amplifying manner. To construct the platform, the primary antibody for PSA was firstly immobilized on a O-ring area of a glass slide for recognizing the PSA. The horseradish peroxidase (HRP) and the secondary antibody of PSA (Ab₂) functionalized Au NPs (HRP-Au NPs-Ab₂) were modified on the platform through immunoreaction between PSA and Ab₂. The excellent catalytic effect of Au NPs and HRP on the HRP-Au NPs-Ab₂ to the luminol-H₂O₂ CL system provided the dual-signal amplification for PSA detection. To further enhance the sensitivity, tyramine signal amplification (TSA) strategy was introduced: tyramine-HRP conjugates were added into the O-ring reservoir and thus tyramine-HRP repeats formed in the presence of H₂O₂, generating a multiple signal amplification because of the large amounts of HRP on the sensing interface. The excellent performance of HRP-Au NPs-Ab₂ and TSA strategy endows the CL platform with high sensitivity. The PSA was detected with a photomultiplier tube (PMT) and visually analyzed by a charge coupled device (CCD), respectively. The linear ranges of PMT and CCD for PSA are 0.1-100.0 ng mL^-1 with a detection limit of 0.05 pg mL^-1 and 0.5 - 100.0 ng mL^-1 with a detection limit of 0.1 pg mL^-1, respectively. The levels of PSA in several human serum samples were determined and the recoveries are ranged from 82.5% - 117.0%. This CL immunosensing platform holds great potential for bioactive molecules detection visually and sensitively.

Ensuring seafood safe to spoon: a brief review of biosensors for marine biotoxin monitoring

With harmful algal blooms, marine food poisoning caused by marine biotoxins frequently occurs and is life-threatening if severe. However, the conventional detection methods of marine toxins have a few limitations: low sensitivity and high-cost. Therefore, it is necessary to establish a fast and sensitive on-site detection method for real seafood sample. Biosensors based on aptamers, antibodies, and cells have been applied in marine toxins monitoring. This review presents the classification and toxic effects of marine toxins, and recent biosensor for marine toxin detection. In addition, we have compared the superiority and limitation of these biosensors. Finally, challenges and opportunities of biosensors in food safety detection were discussed. Considering the excellent results achieved by the aptasensor in the field of detection, it seems ready to be put into practical applications.

Ultra-sensitive and selective electrochemical biosensor with aptamer recognition surface based on polymer quantum dots and C60/MWCNTs- polyethylenimine nanocomposites for analysis of thrombin protein

In this study, an ultra-sensitive and selective Thrombin biosensor with aptamer-recognition surface is introduced based on carbon nanocomposite. To prepare the this biosensor, screen-printed carbon electrodes (SPCE) were modified with a nanocomposite made from fullerene (C₆₀), multi-walled carbon nanotubes (MWCNTs), polyethylenimine (PEI) and polymer quantum dots (PQdot). The unique characteristics of each component of the C₆₀/MWCNTs-PEI/PQdot nanocomposite allow for synergy between nanoparticles while polymer quantum dots resulted in characteristics such as high stability, high surface to volume ratio, high electrical conductivity, high biocompatibility, and high mechanical and chemical stability. The large number of amine groups in C₆₀/MWCNTs-PEI/PQdot nanocomposite created more sites for better covalent immobilization of amino-linked aptamer (APT) which improved the sensitivity and stability of the aptasensor. Differential Pulse Voltammetry (DPV) method with probe solution was used as the measurment method. Binding of thrombin protein to aptamers immobilized on the transducer resulted in reduced electron transfer at the electrode/electrolyte interface which reduces the peak current (I_P) in DPV. The calibration curve was drawn using the changes in the peak current (ΔI_P),. The proposed aptasensor has a very low detection limit of 6 fmol L^-1, and a large linear range of 50 fmol L^-1 to 20 nmol L^-1. Furthermore, the proposed C₆₀/MWCNTs-PEI/PQdot/APT aptasensor has good reproducibility, great selectivity, low response time and a good stability during its storage. Finally, the application of the proposed aptasensor for measuring thrombin on human blood serum samples was investigated. This aptasensor can be useful in bioengineering and biomedicine applications as well as for clinical studies.

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.

Actively targeted gold nanoparticle composites improve behavior and cognitive impairment in Parkinson's disease mice

Parkinson's disease (PD) is characterized by motor and non-motor symptoms, primarily affecting dopaminergic neurons (DAergic neurons) in substantia nigra (SN). However, it is still very challenging to identify new drugs that not only inhibit motor dysfunction but also improve non-motor dysfunction. It has been identified as a potential PD treatment that the inhibition of α-syn aggregation could decrease the death of DAergic neurons in SN. In this study, we synthesized gold nanoparticle composites (NPs) that were loaded with plasmid DNA (pDNA) to inhibit α-syn expression. In vivo, our results showed that NPs improved tyrosine hydroxylase (TH) levels and decreased aggregation of α-syn in the SN. Additionally, NPs attenuated motor dysfunction and exploration ability declined. Moreover, NPs reversed the inhibition of long-term potentiation (LTP) and improved non-motor dysfunction in PD mice. These results indicated that NPs had significantly neuroprotective effects not only in motor, but also in non-motor dysfunction to PD mice, providing a new strategy for gene therapy in PD.

Engineering of exosome-triggered enzyme-powered DNA motors for highly sensitive fluorescence detection of tumor-derived exosomes

Tumor-derived exosomes containing multiple proteins originating from parent cancer cells have emerged as biomarkers for cancer diagnosis. Herein, we propose a three-dimensional DNA motor-based exosome assay platform for the selective and sensitive detection of exosomes. The DNA motor used gold nanoparticle (GNP) tracks, consisting of fluorescein-labeled substrate strands and aptamer-locked motor strands. Recognition of the target protein on exosomes by its aptamer unlocked the motor strand and triggered the DNA motor process. Powered by restriction endonuclease, the motor strands autonomously walked along the GNP track. Each movement step cleaved one substrate strand and restored one fluorescein molecule. For exosome detection, the proposed method displayed a broad dynamic range acrossing 5 orders of magnitude with the detection limit as low as 8.2 particles/μL in PBS. The method also exhibited good selectivity among different tumor-derived exosomes and performed well in complex biological samples. The capability to profile exosomal surface proteins efficiently endowed our DNA motor great potential for developing a simple and cost-effective device for clinical diagnosis.

A fluorometric assay of thrombin using magnetic nanoparticles and enzyme-free hybridization chain reaction

A fluorescence method based on functionalized magnetic nanoparticles (FMNPs) and hybridization chain reaction (HCR) is developed for the enzyme-free amplified determination of thrombin. In the proposed design, aptamer against thrombin was hybridized with the capture DNA-modified magnetic nanoparticles to yield the FMNPs. In the presence of thrombin, aptamers are released due to the specific and high-affinity binding between thrombin and its aptamer. The exposed capture DNA subsequently hybridized with the partial sequence of helper DNA, and the vacant sequence of helper DNA further hybridized with HCR products which is pre-formed by the alternate hybridization of single-stranded DNAs (H1 and H2). The immobilized HCR products were then labeled with YOYO-1 for fluorescence measurement. Fluorescence signal intensity of labeled YOYO-1 was measured at an emission wavelength of 519 nm (excitation under 488 nm) and used for calibration. By taking advantage of HCR amplification, this direct assay strategy showed a linear response in the 20- to 200-pM concentration range, and the limit of detection is 9.2 pM which is about 3-orders of magnitude lower than the serum thrombin concentration (10 nM) that triggers blood clotting. This developed method can efficiently differentiate the target protein from a protein matrix, and it is verified by determination of thrombin in spiked serum samples with recoveries in the range of 94.5-103.3%. Graphical abstract A fluorometry method for thrombin detection using magnetic nanoparticles and enzyme-free hybridization chain reaction.

Gold nanoparticle/MXene for multiple and sensitive detection of oncomiRs based on synergetic signal amplification

Multiple and sensitive detection of oncomiRs for accurate cancer diagnostics is still a challenge. Here, a synergetic amplification strategy was introduced by combining a MXene-based electrochemical signal amplification and a duplex-specific nuclease (DSN)-based amplification system for rapid, attomolar and concurrent quantification of multiple microRNAs on a single platform in total plasma. Synthesized MXene-Ti₃C₂T_x modified with 5 nm gold nanoparticles (AuNPs) was casted on a dual screen-printed gold electrode to host vast numbers of DNA probes identically co-immobilized on dedicated electrodes. Interestingly, presence of MXene provided biofouling resistance and enhanced the electrochemical signals by almost 4 folds of magnitude, attributed to its specious surface area and remarkable charge mobility. The 5 nm AuNPs were perfectly distributed within the whole flaky architect of the MXene to give rise to the electrochemical performance of MXene and provide the thiol-Au bonding feature. This synergetic strategy reduced the DSN-based biosensors' assay time to 80 min, provided multiplexability, antifouling activity, substantial sensitivity and specificity (single mutation recognition). The limit of detection of the proposed biosensor for microRNA-21 and microRNA-141 was respectively 204 aM and 138 aM with a wide linear range from 500 aM to 50 nM. As a proof of concept, this newly-developed strategy was coupled with a 96-well adaptive sensing device to successfully profile three cancer plasma samples based on their altered oncomiR abundances.

Competitive aptasensor for the ultrasensitive multiplexed detection of cancer biomarkers by fluorescent nanoparticle counting

Cancer biomarker quantification in human serum is of great importance for accurate patient diagnosis and informed clinical management. To date, ultrasensitive multiplexed detection of proteins without amplification is still a major challenge. Herein, we proposed a competitive aptasensor strategy for ultrasensitive multiplexed cancer biomarker detection by fluorescent nanoparticle (FNP) counting. The sequences are designed such that the binding abilities of linker DNA (L-DNA) with DNA-functionalized FNPs (DNA-FNPs) and aptamer are comparable. As long as one target binds with one molecule of aptamer, a signalling FNP forms a sandwich-structured nanocomposite, which was subsequently observed and enumerated with a fluorescence microscope. This 1 : 1 target-to-signal FNP production assured an improved sensitivity, benefiting from the reasonably good brightness and photostability of FNPs. For both singleplexed and multiplexed detection, this proposed strategy achieved an approximately 1000-fold improved limit of detection than the conventional method with the detection volume of 3.2 μL. Notably, the results for carcinoembryonic antigen (CEA) detection obtained directly from 9 human serum samples (colorectal/lung/healthy individuals) were consistent with that obtained by ELISA, showing potential application in clinical diagnosis.

Highly sensitive host-guest mode homogenous electrochemical thrombin signal amplification aptasensor based on tetraferrocene label

The development of sensitive and convenient detection methods to monitor thrombin without the use of enzymes or complex nanomaterials is highly desirable for the diagnosis of cardiovascular diseases. In this article, tetraferrocene was first synthesized and then a sensitive and homogeneous electrochemical aptasensor was developed for thrombin detection based on host-guest recognition between tetraferrocene and β-cyclodextrin (β-CD). In the absence of thrombin, the double stem-loop of thrombin aptamer (TBA) prevented tetraferrocenes labeled at both ends from entering the cavity of β-CD deposited on gold electrode surface. After binding with thrombin, the stem-loop structure of TBA opened and transformed into special G-quarter structure, forcing tetraferrocene into the cavity of β-CD. As a result, thrombin allowed eight ferrocene molecules to reach the gold electrode surface, greatly amplifying the response signal. The obtained aptasensors showed dynamic detection range from 4 pM to 12.5 nM with detection limit around 1.2 pM. Overall, the results indicate that the proposed aptasensors are promising for future rapid clinical detection of thrombin and development of signal amplification strategies for detection of various proteins.

A review: Recent advances in ultrasensitive and highly specific recognition aptasensors with various detection strategies

One of the most studied topics in analytical chemistry and physics is to develop bio-sensors. Aptamers are small single-stranded RNA or DNA oligonucleotides (5-25 kDa), which have advantages in comparison to their antibodies such as physicochemical stability and high binding specificity. They are able to integrate with proteins or small molecules, including intact viral particles, plant lectins, gene-regulation factor, growth factors, antibodies and enzymes. The aptamers have reportedly shown some unique characteristics, including long shelf-life, simple modification to provide covalent bonds to material surfaces, minor batch variation, cost-effectiveness and slight denaturation susceptibility. These features led important efforts toward the development of aptamer-based sensors, known as apta-sensors classified into optical, electrical and mass-sensitive based on the signal transduction mode. This review provided a number of current advancements in selecting, development criteria, and aptamers application with the focus on the effect of apta-sensors, specifically for disease-associated analyses. The review concentrated on the current reports of apta-sensors that are used for evaluating different food and environmental pollutants.

A highly sensitive electrochemical biosensor for protein based on a tetrahedral DNA probe, N- and P-co-doped graphene, and rolling circle amplification

A tetrahedral DNA probe can effectively overcome the steric effects of a single-stranded probe to obtain well-controlled density and minimize nonspecific adsorption. Herein, a highly sensitive electrochemical biosensor is fabricated for determination of protein using a tetrahedral DNA probe and rolling circle amplification (RCA). N- and P-co-doped graphene (NP-rGO) is prepared, and AuNPs are then electrodeposited on it for DNA probe immobilization. Benefitting from the synergistic effects of the excellent electrical conductivity of NP-rGO, the stability of the tetrahedral DNA probe and the signal amplification of RCA, the biosensor achieves a low limit of 3.53 × 10^-14 M for thrombin and a wide linear range from 1 × 10^-13 to 1 × 10^-7 M. This study provides a sensitive and effective method for the detection of protein in peripheral biofluids, and paves the way for future clinical diagnostics and treatment of disease. Graphical abstract.

Au–Hg/rGO with enhanced peroxidase-like activity for sensitive colorimetric determination of H2O2

Au–Hg/rGO is applied as a novel nanozyme to construct a sensitive sensing platform for the colorimetric determination of H₂O₂.

A high-energy sandwich-type self-powered biosensor based on DNA bioconjugates and a nitrogen doped ultra-thin carbon shell

A high-energy self-powered sensing platform for the ultrasensitive detection of proteins is developed based on enzymatic biofuel cells (EBFCs) by using DNA bioconjugate assisted signal amplification.

A novel nitrogen and sulfur co-doped carbon dots-H2O2 chemiluminescence system for carcinoembryonic antigen detection using functional HRP-Au@Ag for signal amplification

A novel nitrogen and sulfur co-doped carbon dots (NS-CDs)-H₂O₂ chemiluminescence (CL) system was developed to detect carcinoembryonic antigen (CEA) by taking advantage of dual-signal amplification of functional Au@Ag nanoparticles (NPs) nanoprobes. Horseradish peroxidase (HRP) and the complementary DNA were co-immobilized onto Au@Ag NPs surface to shape the functional nanoprobes (HRP-Au@Ag-cDNA) for signal amplification. In this proposal, HRP-Au@Ag-cDNA was specifically hybridized with CEA aptamer-functionalized magnetic beads to form the double-strand hybridization nanocomposites (HRP-Au@Ag-dsDNA-MB). Upon the addition of CEA, the CEA aptamer preferred to bind with CEA instead of double-strand hybridization interaction, thus HRP-Au@Ag-dsDNA-MB was dehybridized and the HRP-Au@Ag-cDNA nanoprobe was released. The synergistic catalytic effects of HRP and Au @Ag NPs endow the nanoprobe producing a dual CL signal amplification in the NS-CDs-H₂O₂ CL system. The CL intensity of the developed strategy enhanced with CEA concentration increasing in the range of 0.3-80 ng mL^-1. Benefiting from the synergistic effect, a detection limit as low as 94 pg mL^-1 was obtained. Moreover, successful application of this CL sensing platform was achieved for the determination of CEA in human serum samples, demonstrating the promising prospect in the early tumor warning and therapeutic monitoring.

Aptamer-based thin film gold electrode modified with gold nanoparticles and carboxylated multi-walled carbon nanotubes for detecting oxytetracycline in chicken samples

In this work, a disposable and portable aptasensor for the fast and sensitive detection of oxytetracycline (OTC) using gold nanoparticles (AuNPs)/carboxylated multi-walled carbon nanotubes (cMWCNTs)@thionine connecting complementary strand of aptamer (cDNA) as signal tags was constructed. The substrate electrode of the aptasensor was thin film gold electrode (TFGE), which have the advantages of portable and uniform performance. In the presence of OTC, OTC competed with cDNA to combine with aptamer. The bioconjugate (AuNPs/cMWCNTs/cDNA@thionine) was released from the TFGE. Thus, the electrochemical signal declined. Under optimized conditions, the aptasensor exhibited good stability, high selectivity and high sensitivity. Furthermore, the developed electrochemical aptamer-based TFGE had a wide dynamic range of 1 × 10^-13-1 × 10^-5 g mL^-1 for target OTC with a low detection limit of 3.1 × 10^-14 g mL^-1 and was successfully used for the determination of OTC in chicken sample.

Relay-race RNA/barcode gold nanoflower hybrid for wide and sensitive detection of microRNA in total patient serum

Development of a very sensitive biosensor is accompanied with an inevitable shrinkage in the linear detection range. Here, we developed an electrochemical biosensor with a novel methodology to detect microRNA-21 (miR21) at an ultralow level and broad linear detection range. A three-way junction RNA structure was designed harboring (i) a methylene blue (MB)-modified hairpin structure at its one leg to function as the sensing moiety and (ii) the other two legs to be further hybridized with barcode gold nanoparticles (MB/barG) as the signal amplifiers. Addition of target miR21 resulted in opening the hairpin moiety and subsequent hybridization with DNA-modified gold nanoflower/platinum electrode (GNF@Pt) to form the MB-3 sensor. Inspired by the relay-race run, to extend the dynamic detection range and increase the sensitivity of the biosensor, MB/barG was added to form the second detection modality (MBG-3). The combined sensor required very low sample volume (4 μL) and could identify 135 aM or 324 molecules of miR21 with the ability to operate within a wide linear range from 1 μM down to 500 aM. The fabricated GNF@Pt showed a remarkable conductivity compared with the gold nanoparticle-modified electrode. Addition of MB/barG boosted the electrochemical signal of the MB by almost 230 times. Moreover, a new protocol was introduced by the authors to increase the efficiency of microRNA extraction from the total serum. Possessing a sound selectivity and specificity towards single base-pair mutations, the developed biosensor could profile cancer development stages of two patient serums.

An amperometric zearalenone aptasensor based on signal amplification by using a composite prepared from porous platinum nanotubes, gold nanoparticles and thionine-labelled graphene oxide

The authors constructed a voltammetric zearalenone (ZEN) aptasensor based on use of porous platinum nanotubes, gold nanoparticles (p-PtNTs/AuNPs) and thionine (Thi) labelled graphene oxide (GO). The p-PtNTs were synthesized in-situ based on tellurium nanowires as sacrificial templates. Subsequently, thiol-modified aptamers were self-assembled on the AuNPs that had been electrodeposited on the surface of the modified electrode. The presence of p-PtNTs on the electrode increases the loading with AuNPs and aptamers. It also warrants that the Thi-labelled GO can be assembled onto the aptamer via π interactions. In the presence of ZEN, it will be bound by the aptamer. The GO/Thi conjugate will be released from the aptamer, and this causes a decrease in Thi current. Under the optimal conditions and at a typical working potential of -0.22 V (vs. Ag/AgCl), the method has a linear range that covers the 0.5 pg·mL^-1 to 0.5 μg·mL^-1 ZEN concentraion range and a lower detection limit of 0.17 pg·mL^-1. Graphical abstract Voltammetric zearalenone aptasensor based on use of porous platinum nanotubes/gold nanoparticles and thionine labelled graphene oxide was fabricated for the detection of zearalenone.

A label-free fluorometric aptasensor for adenosine triphosphate (ATP) detection based on aggregation-induced emission probe

Based on Aggregation-Induced Emission (AIE), the development of a label-free, simple and sensitive fluorometric aptasensor for adenosine triphosphate (ATP) detection is described. With ATP present, the aptamers will combine with ATP and the conformation of the aptamer will switch from a random coil to an antiparallel G-quadruplex, which impedes the digestion by exonuclease I (Exo I). Addition of 4,4 -(1E,1E)-2,2-(anthracene-9,10-diyl) bis (ethene-2,1-diyl) bis (N,N, N-trimethyl-benzenaminium iodide) (DSAI) into the solution will cause aggregation of DSAI on the surface of the aptamer/ATP complex and consequently give rise to strong emission. Additionally, a good linear relationship was observed under optimized conditions between the fluorescence intensities and the logarithm of ATP concentrations (R² = 0.9908). The established aptamer sensor was highly sensitive and exhibited a low limit of detection of 32.8 nM, with superior specificity for ATP. It was also used in the quantification of ATP levels in human serum samples and demonstrated satisfactory recoveries in the scope of 93.2%-107.6%. The cellular ATP assay results indicated that the developed method can be used for monitoring ATP concentrations in cell extracts without the interference of other substances in the cells. This method offers several advantages such as simplicity, rapidity, low cost and excellent selectivity, which make it hold great potential for the detection of ATP in bioanalytical and biological studies.

A label-free and double recognition-amplification novel strategy for sensitive and accurate carcinoembryonic antigen assay

Herein, a label-free and double recognition-amplification (LDRA) strategy for carcinoembryonic antigen (CEA) detection was developed, based on a new designed dual-function messenger probe (DMP) coalescing with DNA tetrahedron probes (DTPs) and hybridization chain reaction (HCR). The DMP possess dual-function to replace CEA for specific interface hybridization and initiate hybridization chain reaction. The interfacial hybridization event was quantitatively converted to an electrochemical signal by using hemin/G-quadruplex (h-Gx) formed after the hybridization chain reaction. Self-assembled DNA tetrahedron probes, which were readily decorated on an electrode surface as a scaffold with rigid support and ordered orientation, enabled the highly efficient strands hybridization and greatly increased target accessibility as well as significantly decreased noise. The proposed assay integrated dual recognition processes and HCR signal amplification processes, achieving the identification of low concentration of CEA as detection limit of 18.2 fg mL^-1 (S/N = 3) and wider linearity range of 0.0001 ng mL^-1-50 ng mL^-1. A new electrochemical sensing method was proposed for CEA detection and used in real clinical samples. The obtained results were good consistency with those of clinical diagnosis.

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

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

Recent advances in nanomaterial-based electrochemical and optical sensing platforms for microRNA assays

This review describes recent efforts in the application of nanomaterials as sensing elements in electrochemical and optical miRNAs assays.