Strand Displacement-Induced Enzyme-Free Amplification for Label-Free and Separation-Free Ultrasensitive Atomic Fluorescence Spectrometric Detection of Nucleic Acids and Proteins

Cascade signal amplification using Hg2+-induced oxidation of silver nanoparticles and cation exchange reaction for ICP-MS bioassay

Combining the Hg2+-induced oxidization of silver nanoparticles with the cation exchange reaction between Ag+ and CuS nanoparticles for cascade signal amplification, a sensitive, universal and label-free ICP-MS bioassay for nucleic acids and proteins was developed. By replacing the loop sequence of the T-Hg-T hairpin structure with specific sequences or aptamers to different biomarkers, it has great promise for the early detection of biomarkers potentially for diagnosis of cancerous diseases.

Enzyme-free nucleic acid dual-amplification strategy combined with mimic enzyme catalytic precipitation reaction for the photoelectrochemical detection of microRNA-21

A novel photoelectrochemical (PEC) biosensor based on an enzyme-free nucleic acid dual-amplification strategy combined with a mimic enzyme to catalyze the deposition of a quencher is reported for the ultrasensitive detection of miRNA-21. A limited amount of target miRNA-21 can trigger the formation of long DNA duplexes on the electrode, owing to the synergistic effect of the enzyme-free nucleic acid dual-amplification strategy of entropy-driven strand displacement reaction (ESDR) amplification and hybridization chain reaction (HCR) amplification. The embedded manganese porphyrin (MnPP) in the long DNA duplexes acts as a horseradish peroxidase (HRP)-mimicking enzyme to catalyze the transformation of benzo-4-chlorohexadienone on the electrode surface, resulting in a significant reduction in photocurrent intensity. As a photosensitive material, BiOCl-BiOI is used as a tag to provide strong initial PEC signals. Based on the cascade integration of the enzyme-free nucleic acid dual-amplification strategy and the mimic enzyme-catalyzed precipitation reaction, the current PEC biosensor exhibits outstanding performance for miRNA-21 detection with an ultralow detection limit (33 aM) and a wide quantification range (from 100 aM to 1 nM). This work provides a new avenue toward the ultrasensitive detection of miRNAs, and is expected to be used for clinical and biochemical samples. A unique PEC biosensor with the BiOCl-BiOI composite, as the photosensitive material, has been developed for ultrasensitive miRNA-21 determination based on the combination of an enzyme-free nucleic acid dual-amplification strategy and mimic enzyme catalytic precipitation reaction.

Isothermal Self-Primer EXPonential Amplification Reaction (SPEXPAR) for Highly Sensitive Detection of Single-Stranded Nucleic Acids and Proteins

Development of versatile sensing methods for sensitive and specific detection of clinically relevant nucleic acids and proteins is of great value for disease monitoring and diagnosis. In this work, we propose a novel isothermal Self-primer EXPonential Amplification Reaction (SPEXPAR) strategy based on a rationally engineered structure-switchable Metastable Hairpin template (MH-template). The MH-template initially keeps inactive with its self-primer overhanging a part of target recognition region to inhibit polymerization. The present targets can specifically compel the MH-template to transform into an "activate" conformation that primes a target-recyclable EXPAR. The method is simple and sensitive, can accurately and facilely detect long-chain single-stranded nucleic acids or proteins without the need of exogenous primer probes, and has a high amplification efficiency theoretically more than 2ⁿ. For a proof-of-concept demonstration, the SPEXPAR method was used to sensitively detect the characteristic sequence of the typical swine fever virus (CSFV) RNA and thrombin, as nucleic acid and protein models, with limits of detection down to 43 aM and 39 fM, respectively, and even the CSFV RNA in attenuated vaccine samples and thrombin in diluted serum samples. The SPEXPAR method may serve as a powerful technique for the biological research of single-stranded nucleic acids and proteins.

Multifunctional electrochemical biosensor with "tetrahedral tripods" assisted multiple tandem hairpins assembly for ultra-sensitive detection of target DNA

Nucleic acids are genetic materials in the human body that play important roles in storing, copying, and transmitting genetic information. Abnormal nucleic acid sequences, base mutations, and genetic changes often lead to cancer and other diseases. Meanwhile, methylated DNA is one of the main epigenetic modifications, which is considered to be an excellent biomarker in the early detection, prognosis, and treatment of cancers. Therefore, a multifunctional electrochemical biosensor was constructed with sturdy tetrahedral tripods, which assisted multiple tandem hairpins through base complementary pairing and effective ultra-sensitive detection of targets (DNA, microRNA, and methylated DNA). In the experiments, experimental conditions were optimized, and different DNA concentrations in serum were detected to verify the sensitivity of the biosensor and the feasibility of this protocol. In addition, microRNA and DNA methylation were detected through different designs of tetrahedral tripods (TTs) that capture probes to prove the superiority of this scheme. A sturdy pyramid structure of TTs extremely enhanced the capture efficiency of targets. The targets triggered the one-step isothermal multi-tandem amplification reaction by incubating multiple hairpin assemblies. To our knowledge, a combination of two parts, which greatly reduced background interference and decreased non-specific substance interference, has appeared for the first time in this paper. Moreover, the load area of electrochemical substances was significantly increased than that in previous studies. This greatly increased the detection range and detection limit of targets. The electrochemical signal responses were generated in freely diffusing hexaammineruthenium(iii) chloride (RuHex). RuHex could adhere to the DNA phosphate backbone by a powerful electrostatic attraction, causing increased current responses.

Schematic illustration of the fabricated electrochemical biosensor. TTs assisted multiple tandem hairpins assembly for ultra-sensitive detection of target DNA.

Filter-Assisted Separation of Multiple Nanomaterials: Mechanism and Application in Atomic/Mass Spectrometry/Fluorescence Label-Free Multimode Bioassays

Atomic spectrometry (AS) has been widely used in bioassay, but it requires steps to immobilize or separate the signal molecules. In this work, based on the phenomenon that the filter membrane can selectively separate multiple nanomaterials (nanoparticles (NPs) and quantum dots (QDs)) and its related ions, including poly(thymine)-templated Cu NPs and free Cu²⁺, Ag NPs and free Ag⁺, CdTe QDs and Cd²⁺, we constructed multimode and label-free biosensors by chemical vapor generation-atomic fluorescence spectrometry (CVG-AFS), inductively coupled plasma mass spectrometry (ICP-MS), and fluorescence. In this strategy, terminal deoxynucleotidyl transferase (TdT) and polynucleotide kinase (PNK), H₂O₂, and mucin 1 can be sensitively detected using Cu²⁺, Ag⁺, and Cd²⁺ as the signal probe, respectively. As a result, TdT and T4 PNK in single cells level can be accurately quantified. In addition, the possible separation mechanism of filter membrane was proposed, both Donnan repulsion by charged functional layer and entrapment effect by nanomaterials size contributed to the outstanding separation performance. Subsequently, on the basis that CdTe QDs can selectively identify Cu NPs/Cu²⁺, Ag NPs/Ag⁺, and C-Ag⁺-C/Ag⁺, cation-exchange reaction (CER) was introduced in this platform due to its unique advantages, including improving the sensitivity of the above system (an order of magnitude), converting the non-CVG metal elements into CVG elements, and using low-cost AFS to substitute the high-cost ICP-MS. In addition, we performed theoretical calculations of the selective CER using density functional theory (DFT). Therefore, this label-free and simple separation AS/ICP-MS sensing platform shows great potential for biomarker analysis.

Visual and dual-fluorescence homogeneous sensor for the detection of pyrophosphatase in clinical hyperthyroidism samples based on selective recognition of CdTe QDs and coordination polymerization of Ce3+

A visual / dual fluorescent strategy based on selective recognition of QDs and coordination polymerization of Ce³⁺ was developed for pyrophosphatase detection.

Homogeneous assay based on the pre-reduction and selective cation exchange for detection of multiple targets by atomic spectrometry

In view of the high sensitivity and good selectivity, chemical vapor generation atomic spectrometry (CVG-AS) and inductively coupled plasma mass spectrometer (ICP-MS), especially low-cost atomic fluorescence spectrometry (AFS) have been widely used in bioassay. However, the existing AS method is mostly based on heterogeneous strategies, and can't detect multiple targets in one system. In this study, we present the discovery and mechanism study of a phenomenon of Hg²⁺ pre-reduction that the concentration of Hg²⁺ decreased when it was mixed with the reductants (ascorbic acid (AA), SnCl₂, or NaBH₄/KBH₄) over long-time reaction (hours) by CVG-AFS and ICP-MS. A homogeneous Cu²⁺ assay method was developed based on the competition reaction of Cu²⁺ and Hg²⁺ for consuming AA, and its application in the detection of pyrophosphate (PPi) and alkaline phosphatase (ALP) was investigated based on the PPi complexation with Cu²⁺, and ALP hydrolyzation of PPi using CVG-AFS as a representative detector. Subsequently, in order to further verify the applicability of the system, cation exchange reaction (CER) was utilized here based on the selectively recognize Ag⁺ and C-Ag⁺-C by CuS nanoparticles (NPs). As the exchanged Cu²⁺ from CuS NPs can be sensitively and selectively detected via above-mentioned Cu²⁺ assay method, this strategy can be extended for the Ag⁺, DNA and prostate specific antigen (PSA) detection based on base complementary pairing and the specific recognition of aptamer. Under the optimal experimental conditions, the system showed high sensitivity for the detection of Cu²⁺, PPi, ALP, Ag⁺, DNA, and PSA, with limit of detections (LODs) of 0.12 nmol L^-1, 25 μmol L^-1, 0.025 U/L, 0.2 nmol L^-1, 0.05 nmol L^-1, and 0.03 ng/mL, respectively. The method was successfully used to determination Cu²⁺, ALP, and PSA in human serums, showing similar results with those of ICP-MS and kits methods.

Detection of toxin B of Clostridium difficile based on immunomagnetic separation and aptamer-mediated colorimetric assay

Clostridium difficile can cause antibiotic-associated diarrhoea or pseudo-membranous colitis in humans and animals. Currently, the various methods such as microbiological culture, cytotoxic assay, ELISA and polymerase chain reaction have been used to detect Clostridium difficile infection (CDI). These conventional methods, however, require long detection time and professional staff. The paper is to describe a simple strategy which employs immunomagnetic separation and aptamer-mediated colorimetric assay for the detection of toxin B of C. difficile (TcdB) in the stool samples. HRP-labelled aptamer against TcdB selected by SELEX was firstly captured on the surface of magnetic beads (MB) by DNA hybridization with a complementary strand. In the presence of TcdB, aptamer specifically recognized and bound TcdB, disturbing the DNA hybridization and causing the release of HRP-aptamer from MB. This reduced the catalytic capacity of HRP and consequently the absorption intensity. As there was a relationship between the decrease in the absorption intensity and target concentration, a quantitative analysis of TcdB can be accomplished by the measurement of the absorption intensity. Under the optimal conditions, the assay system is able to detect TcdB at a concentration down to 5 ng ml^-1 . Moreover the method had specificity of 97% and sensitivity of 66% and the system remained excellent stability within 4 weeks. The proposed method is a valuable screening procedure for CDI and can be extended readily to detection of other clinically important pathogens.

Selective recognition of CdTe QDs and strand displacement signal amplification-assisted label-free and homogeneous fluorescence assay of nucleic acid and protein

Due to their simplicity of design and operation, homogeneous bioassays have been of great interest to researchers. Herein, a label-free and free separation fluorescence sensing platform was constructed for the determination of nucleic acid and prostate specific antigen (PSA) using CdTe QDs as the signal molecule. In our previous work, we surprisingly found that the CdTe QDs can selectively distinguish Ag+ and the C-Ag+-C complex, which was the basis of the sensor. On the basis of the selective cation exchange reaction (CER), combined with the signal amplification of the strand displacement reaction (SDR), this work was first applied for the sensitive analysis of DNA. There are two types of hairpin structures in this sensing system, including the recognition probe (HP) and Ag+, which formed the C-Ag+-C structure, and the hairpin structure formed by the helper DNA itself. In this work, target DNA can trigger the SDR that generates lots of HP-helper double-stranded DNA (dsDNA) and recycles the target DNA while releasing a large amount of Ag+, thus quenching the fluorescence signal of CdTe QDs to achieve the highly sensitive detection of DNA. In order to verify the versatility of this system using DNA as a bridge and aptamers as recognition probes, we extended the system to the detection of PSA. After examining its experimental performance, it was determined that this method displayed good analytical capability for DNA in the range of 10-13-10-10 M and PSA in the range of 10-13-10-10 g mL-1 with low 25 fM and 30 fg mL-1 limits of detection (LODs), respectively; high selectivity for both the target sequence and protein was shown. In addition, this platform was successfully used for the analysis of PSA in serum samples.

A visual detection of human immunodeficiency virus gene using ratiometric method enabled by phenol red and target-induced catalytic hairpin assembly

Relying on the specific coordination of Ag⁺ and mismatched cytosine-cytosine (C-C), the high-efficiency inhibition of urease by Ag⁺ ion, and the rapid and sensitive response of phenol red to pH, a sensitive ratiometric sensor has been designed for visual detection of human immunodeficiency virus gene (HIV DNA). This sensor utilizes the HIV DNA to initiate catalytic hairpin assembly (CHA) process, releasing Ag⁺ to inhibit subsequent urease-catalyzed urea hydrolysis and prevent the pH of the solution from rising. The CHA process and the absorbance ratio of phenol red at different wavelengths (A₅₅₉/A₄₃₂) amplify the signal, allowing the sensor to detect HIV DNA from 10 to 130 nM in a sensitive and highly selective manner with a low detection limit of 7.8 nM. In addition, this sensor can visually distinguish different concentrations of HIV DNA within a certain range and possesses a good recovery in 1% of serum samples, which will provide new ideas for biosensor design, dipstick test, blood test, and other clinical disease prevention.

Thiol inhibition of Hg cold vapor generation in SnCl2/NaBH4 system: A homogeneous bioassay for H2O2/glucose and butyrylcholinesterase/pesticide sensing by atomic spectrometry

Recently, the use of atomic spectrometry (AS) for biochemical analysis has attracted considerable attention due to its high sensitivity, selectivity and anti-interference ability. In this work, we conducted a detailed study on a phenomenon of thiol inhibition of mercury (Hg²⁺) cold vapor generation (CVG) and found _L-cysteine (_L-Cys), glutathione (GSH), dithiothreitol, N-Acetyl-L-cysteine, 3-mercaptopropionic acid, β-mercaptoethanol, and NaI can inhibit the CVG of Hg²⁺, while EDTA has no inhibitory effect. Furthermore, changing the content of -SH can effectively adjust the CVG atomic fluorescence spectrometer (CVG-AFS) signal of Hg²⁺. As as a consequence, an AS-based homogeneous bioassay was constructed by adjusting the oxidation ratio and production quantity of -SH in the system. The quantitative analysis of the system was demonstrated by using AFS as a representative detector. Hydrogen peroxide (H₂O₂) and glucose were used as representative analytes for the validation of Hg²⁺ atomic fluorescence signal turn-off strategy, and butyrylcholinesterase (BChE) as well as parathion (organophosphorus pesticides, OPs) as utilized as representative targets for the signal turn-on strategy. Under optimal experimental conditions, the homogeneous CVG-AFS sensor can be successfully used to detect 3 μM H₂O₂, 30 μM glucose, 0.25 U/L BChE, and 0.4 μg/mL parathion. In addition, the detection results of glucose and BChE in human serum samples agreed well with those obtained by using glucometer and kit, showing the promising potential of this method for practical applications. Therefore, this work provides a perspective for the construction of AS-based homogeneous bioassays and shows great potential for the detection of biomarkers.

Sensitive CVG-AFS/ICP-MS label-free nucleic acid and protein assays based on a selective cation exchange reaction and simple filtration separation

Nowadays, label-free atomic spectrometric bioassays are attracting great research interest because of their advantages of low cost, simple design and operation, etc. Herein, a novel and simple chemical vapor generation-atomic fluorescence spectrometry (CVG-AFS)/inductively coupled plasma-mass spectrometry (ICP-MS) label-free detection method is presented for highly sensitive and selective assay of DNA and proteins. This work mainly combined a phenomenon that CdTe quantum dots (QDs) can be used to selectively differentiate free Hg2+ and the T-Hg2+-T complex, with the use of simple membrane filtration separation to improve the performance of the label-free bioassay methods. Upon hybridization with the DNA/protein (carcinoembryonic antigen, CEA) target, the T-Hg2+-T hairpin structure was opened and Hg2+ was released; this initiated the cation exchange reaction between Hg2+ and CdTe QDs which released Cd2+ simultaneously. Subsequently, the free Cd2+ was separated by the filtration membrane without separating the CdTe QDs, which could then be separated from the sample matrices for the CVG-AFS/ICP-MS assay. Under the optimal conditions, this method possessed high sensitivity for DNA and CEA determination with limits of detection (LODs) of 0.2 nM and 0.2 ng mL-1, and linear dynamic ranges of 1-160 nM and 0.5-20 ng mL-1, respectively, and exhibited excellent DNA sequence specificity and protein selectivity. This method preserves the advantages of the label-free atomic spectrometric bioassay, and combined with the selective cation exchange reaction and simple filtration separation to improve the performance.

Visual/CVG-AFS/ICP-MS multi-mode and label-free detection of target nucleic acids based on a selective cation exchange reaction and enzyme-free strand displacement amplification

Visual/CVG-AFS/ICP-MS three-mode detection of DNA based on the selective cation exchange reaction and enzyme-free strand displacement amplification.

Applying strand displacement amplification to quantum dots-based fluorescent lateral flow assay strips for HIV-DNA detection

Up to now, the colloidal gold labeling immunochromatographic test strip is a mature and applicable technology. However, different from the conventional gold nanoparticle, quantum dot (QD) possesses larger specific surface area and better biocompatibility. So, as a novel nanomaterial, QD is capable of assembling more biomolecule which could enhance the sensitivity and accuracy of strips by rationality. Besides, strand displacement amplification was drawn into our test strips in this paper, this assumption made HIV-DNA recycling many times and converting it to plentiful QD-dsDNA (double-stranded deoxyribonucleic acid), where after these nano-structures would be captured by test zone. Meanwhile, the suggested scheme eliminated the hook effect owing to the target drop out of the incorporation on test zone, and any nucleotide sequence or substance which has aptamers can work as the target, such as carcinoembryonic antigen or mycotoxin. This assay realized the detection limit of as low as 0.76 pM (S/N = 3) and the detection range of 1 pM to 10 nM. In the end, we made use of this fluorescent lateral flow assay strips with great reproducibility for detecting HIV-DNA in human serum, that attested this method could be applied to practical application prospectively.

A homogeneous electrochemical sensor for Hg2+ determination in environmental water based on the T-Hg2+-T structure and exonuclease III-assisted recycling amplification

A simple, fast, sensitive, and homogeneous electrochemical sensor based on the T-Hg2+-T structure and exonuclease III-assisted recycling amplification has been constructed for mercury ion (Hg2+) detection. The cT and methylene blue-labeled DNA probes (MB-TDNA) were designed to contain poly T sequences, which were repulsed from the negatively charged indium tin oxide (ITO) electrode due to their abundant negative charges. Hg2+ could trigger the formation of double-stranded DNA (dsDNA) between two DNA probes owing to the stable T-Hg2+-T structure. Then, Exo III specifically recognizes the cleavage of the double-stranded structure to release a methylene blue-labeled mononucleotide fragment (MB-MF). Moreover, the release of the target Hg2+ induces new hybridization and produces a large number of MB-MFs; MB-MFs are not repulsed by the negatively charged ITO electrode surface, thus producing a significant current signal. Under optimal conditions, the differential pulse voltammetric (DPV) response had a linear relationship with the logarithm of Hg2+ concentration in the range of 1.0 nM-0.5 μM, and the proposed method displayed great applicability for detecting Hg2+ in tap-water samples.

Enzyme-free Target Recycling and Double-Output Amplification System for Electrochemiluminescent Assay of Mucin 1 with MoS2 Nanoflowers as Co-reaction Accelerator

In this work, a sensitive electrochemiluminescent assay of mucin 1 (MUC1) was developed with the advantages of target recycling amplification strategy and effective MoS₂ nanoflower (MoS₂ NF)-based signal probe. Briefly, the target MUC1 triggered enzyme-free recycling and a double-output amplification process was executed to acquire masses of single-stranded DNA as a mimic target, which further participated in the catalytic hairpin assembly process for signal amplification. Meanwhile, MoS₂ NFs were prepared as an effective co-reaction accelerator, which not only possessed excellent catalytic performance for H₂O₂ decomposition to largely enhance the luminous intensity of N-(aminobutyl)- N-(ethylisoluminol) (ABEI)-H₂O₂ electrochemiluminescence system but also offered a desirable platform for ABEI-functionalized Ag nanoparticles (ABEI-Ag complexes) loading via Ag-S binding. The experimental results showed the proposed aptasensor had a good linear relationship in the range of 1 fg/mL to 10 ng/mL for MUC1 detection and the limit of detection was 0.58 fg/mL (S/N = 3). In addition, the aptasensor had nice stability and selectivity and huge potential to be applied in clinical research.

Detection of nucleic acids via G-quadruplex-controlled l-cysteine oxidation and catalyzed hairpin assembly-assisted signal amplification

A novel homogeneous strategy for detection of DNA via biomimetic synthesis of luminescent QDs coupled with nucleic acid signal amplification.

Selective reduction-based, highly sensitive and homogeneous detection of iodide and melamine using chemical vapour generation-atomic fluorescence spectrometry

A selective reduction-based method was proposed for the sensitive detection of iodide and melamine using chemical vapour generation (CVG) coupled with atomic fluorescence spectrometry (AFS).

Highly effective molecule converting strategy based on enzyme-free dual recycling amplification for ultrasensitive electrochemical detection of ATP

An enzyme-free and highly effective molecule converting strategy was described for the sensitive electrochemical detection of ATP based on target-driven catalytic hairpin assembly and Mg²⁺-dependent DNAzymes.