Hybridization chain reaction-based colorimetric aptasensor of adenosine 5'-triphosphate on unmodified gold nanoparticles and two label-free hairpin probes

Cascade branch migration-triggered strand displacement amplification for specific and sensitive detection of microRNA

MicroRNAs (miRNAs) have been involved in many biological processes and are regarded as promising biomarkers. The short sequence, low abundance and highly homologous interference sequences greatly hinder the accurate detection of miRNAs. Here, a cascade branch migration-triggered strand displacement amplification (CBM-TSDA) strategy was developed for the first time for specific and sensitive detection of miRNA-155 (miR-155). In the presence of target miR-155, the CBM was initiated and two Y-shaped probes were eventually produced. Next, the Y-shaped probes were transformed into three-way junction (3WJ) structures and triggered the SDA to produce a large number of G-quadruplex (G4) structures. Finally, the increased fluorescence signal of G4/Thioflavin T (ThT) was used to quantify miR-155. Meanwhile, the colorimetric responses of the G4-hemin DNAzyme could be used as supplementary detection to obtain a dual-mode signal readout. This detection strategy showed high detection sensitivity, and the limit of detection was 0.28 pM in the fluorescence detection mode and 0.34 pM in the colorimetric detection mode. Notably, it showed high detection specificity, being able to discriminate the single-base mutations of the target with a high discrimination factor. The strategy also possessed excellent capacity for miR-155 detection in cell lysates and real human blood samples. The developed strategy provides a promising detection platform for miRNA, which may be applied to early clinical diagnosis.

Target-Responsive DNA Nanoclaw for the On-Site Identification of Chinese Medicines with Naked Eye

The identification of Chinese medicinal herbs occupies a crucial part in the development of the food and drug market. Although molecular identification based on real-time PCR offers good versatility and uniform digital standards compared with traditional methods, such as morphology, the dependence on large-scale equipment hinders spot detection and marketable applications. In this study, we developed a DNA nanoclaw for colorimetric detection and visible on-site identification of Chinese medicines. When specific miRNA is present, the DNAzyme is activated and cleaves the substrate strand, triggering the catalytic hairpin assembly (CHA) reaction and forming branched DNA junctions on AuNP-I. This can then capture AuNP-II through hybridization and facilitate their aggregation, resulting in a noticeable color change that is observable to the naked eye. By harnessing the dual amplification of DNAzyme and CHA, this highly sensitive nanoprobe successfully achieved specific identification of Chinese medicines. This offers a new perspective for on-site testing in the herbal market.

Turn-on fluorescent nanoprobe for ATP detection based on DNA-templated silver nanoclusters

A turn-on fluorescence nanoprobe was constructed for the determination of adenosine 5'-triphosphate (ATP) based on DNA-templated silver nanoclusters (DNA-AgNCs). The significant enhancement fluorescence intensity of DNA-AgNCs in the presence of ATP is due to the high special binding affinity between ATP and the aptamer, resulting in the environment of DNA-AgNCs with darkish fluorescence lying at one terminus of DNA slightly altering owing to the change of ATP aptamer conformation. A good linear range runs from 9 to 24 mM with a satisfactory detection limit of 3 μM. Furthermore, the proposed nanoprobe exhibited good performance for ATP detection in diluted fetal bovine serum.

Dumbbell hybridization chain reaction coupled with positively charged Au@luminol nanoparticles for enhanced electrochemiluminescent sensing of exosomal miRNA-21

MicroRNAs (miRNAs) are important cancer biomarkers in cancer cell-derived exosomes. Herein, positively charged Au@luminol nanoparticles ((+)Au@luminol NPs) with enhanced electrochemiluminescence (ECL) and extreme stability were firstly established for the sensitive detection of miRNA-21 in exosome. In the presence of miRNA-21, dumbbell hybridization chain reaction (DHCR) happened at gold nanoparticles and ZIF-67 metal-organic framework modified glass carbon electrode (AuNP/ZIF-MOF/GCE) with the help of dumbbell DNA fuel strands (DHP1 and DHP2). The formed DHCR polymers were negatively charged and could electrostatically adsorb numbers of (+)Au@luminol NPs to produce strong ECL signal. Combing DHCR signal amplification with (+)Au@luminol NPs enhancer, sensitive detection of miRNA-21 realized with a detection limit of 0.43 fM. Moreover, the proposed method was successfully applied for the analysis of miRNA-21 in serum samples of healthy individuals and breast cancer patients, indicating a potential application value in early clinical diagnosis.

Novel fluorescence nano-orbital biosensor for highly sensitive microRNA detection

BACKGROUND

MicroRNAs play an important role in regulating cell function and gene expression. Early prevention and clinical diagnosis of diseases have high requirements for high-sensitivity detection of microRNAs. Due to the limitations of tedious operation and large sample size, miRNA with small molecular weight and low expression abundance cannot be accurately detected in traditional miRNA detection. To improve the sensitivity and accuracy of detection, we established a novel biosensor based on nucleic acid circuit of signal amplification, which converted miRNA recognition into a fluorescence signal for amplification.

RESULTS

We designed a biosensor based on an exponential amplification reaction with cascaded HCR and DNAzyme nucleic acid circuit (named E-NOF biosensor) by amplicon sub-fragments to trigger the construction of fluorescence nano-orbitals (NOF), which could be used to detect miRNA ultrasensitively. By modifying two fluorophores (Cy3 and Cy5) on the chain of constructing nano-orbitals, when the amplicon triggered the construction of nano-orbitals, fluorescence resonance energy transfer (FRET) occurred between Cy3 and Cy5, and then two fluorescence signals with different trends could be observed. Therefore, through the ratio of the two signals, we could quantitatively and quickly detect the miRNA from 1 fM to 100 nM, and the E-NOF biosensor detection limit was as low as 0.129 fM. Furthermore, the HCR nucleic acid circuit cascaded with DNAzyme could enrich the fluorophores on the nano-orbitals and significantly enhance the fluorescence signal by accelerating the reaction rate.

SIGNIFICANCE

According to our understanding, the E-NOF biosensor is the first strategy to cascade EXPAR with HCR and DNAzyme nucleic acid circuit for miRNA-1246 detection. Accurate results can be obtained in only 120 min. Compared with the traditional HCR system, the sensitivity of the new E-NOF biosensor is increased by 1 × 109 times. Furthermore, the biosensor can also detect biomarkers in human serum samples. It has great potential in miRNA detection and identification.

Sensitive and Direct Analysis of Pseudomonas aeruginosa through Self-Primer-Assisted Chain Extension and CRISPR-Cas12a-Based Color Reaction

Pseudomonas aeruginosa (P. aeruginosa) is a common opportunistic Gram-negative pathogen that may cause infections to immunocompromised patients. However, sensitive and reliable analysis of P. aeruginosa remains a huge challenge. In this method, target recognition assists the formation of a self-primer and initiates single-stranded chain production. The produced single-stranded DNA chain is identified by CRISPR-Cas12a, and consequently, the trans-cleavage activity of the Cas12a enzyme is activated to parallelly digest Ag+ aptamer sequences that are chelated with silver ions (Ag+). The released Ag+ reacted with 3,3',5,5'-tetramethylbenzidine (TMB) for coloring. Compared with the traditional color developing strategies, which mainly rely on the DNA hybridization, the color developing strategy in this approach exhibits a higher efficiency due to the robust trans-cleavage activity of the Cas12a enzyme. Consequently, the method shows a low limit of detection of a wide detection of 5 orders of magnitudes and a low limit of detection of 21 cfu/mL, holding a promising prospect in early diagnosis of infections. Herein, we develop a sensitive and reliable method for direct and colorimetric detection of P. aeruginosa by integrating self-primer-assisted chain production and CRISPR-Cas12a-based color reaction and believe that the established approach will facilitate the development of bacteria-analyzing sensors.

Colorimetric Aptasensor for the Visual and Microplate Determination of Clusterin in Human Urine Based on Aggregation Characteristics of Gold Nanoparticles

Clusterin has the potential to become the biomarker of multiple diseases, but its clinical quantitative detection methods are limited, which restricts its research progress as a biomarker. A rapid and visible colorimetric sensor for clusterin detection based on sodium chloride-induced aggregation characteristic of gold nanoparticles (AuNPs) was successfully constructed. Unlike the existing methods based on antigen-antibody recognition reactions, the aptamer of clusterin was used as the sensing recognition element. The aptamer could protect AuNPs from aggregation caused by sodium chloride, but clusterin bound with aptamer detached it from AuNPs, thereby inducing aggregation again. Simultaneously, the color change from red in the dispersed state to purple gray in the aggregated state made it possible to preliminarily judge the concentration of clusterin by observation. This biosensor showed a linear range of 0.02-2 ng/mL and good sensitivity with a detection limit of 5.37 pg/mL. The test results of clusterin in spiked human urine confirmed that the recovery rate was satisfactory. The proposed strategy is helpful for the development of label-free point-of-care testing equipment for clinical testing of clusterin, which is cost-effective and feasible.

A tag-free fluorescent aptasensor for tobramycin detection using a hybridization of three aptamer strands and SYBR Green I dye

In this study, a sensitive fluorescent method is designed to detect tobramycin (TOB) drug applying a hybrid structure of three aptamer strands and SYBR Green I (SGI) fluorescent dye as the bioreceptor segment and signal indicator, respectively. The preferential binding of the aptamers to TOB resulted in the collapse of the hybridized aptamer skeleton to the single strands. So, the intercalation of SGI molecules reduced that quenched the fluorescence response. The aptasensing assay provided the superior target specificity with a detection limit (LOD) of 0.153 pM and a wide linear dynamic range over 0.5 pM-300 μM. The aptasensor could successfully quantify TOB in human serum samples. The tag-free sensor with the remarkable advantages of simplicity, easy-to-use, cost-effectiveness, and high sensitivity is superior to be applicable for clinical samples.

Functional DNA sensors integrated with nucleic acid signal amplification strategies for non-nucleic acid targets detection

In addition to carrying and transmitting genetic material, some DNA molecules have specific binding ability or catalytic function. DNA with this special function is collectively referred to as functional DNA (fDNA), such as aptamer, DNAzyme and so on. fDNA has the advantages of simple synthetic process, low cost and low toxicity. It also has high chemical stability, recognition specificity and biocompatibility. In recent years, fDNA biosensors have been widely investigated as signal recognition elements and signal transduction elements for the detection of non-nucleic acid targets. However, the main problem of fDNA sensors is their limited sensitivity to trace targets, especially when the affinity of fDNA to the targets is low. To further improve the sensitivity, various nucleic acid signal amplification strategies (NASAS) are explored to improve the limit of detection of fDNA. In this review, we will introduce four NASAS (hybridization chain reaction, entropy-driven catalysis, rolling circle amplification, CRISPR/Cas system) and the corresponding design principles. The principle and application of these fDNA sensors integrated with signal amplification strategies for detection of non-nucleic acid targets are summarized. Finally, the main challenges and application prospects of NASAS integrated fDNA biosensing system are discussed.

Nile blue as reporter dye in salt aggregation based-colorimetric aptasensors for peptide, small molecule and metal ion detection

Herein, we report a novel approach for the design of a colorimetric aptasensor, relying on a Dye Salt Aggregation-based Colorimetric Oligonucleotide assay (DYSACO assay). This method is based on the use of an intercalating agent, Nile Blue (NB), whose aggregation capacities (and thus modification of its absorption spectrum) are drastically amplified by adding salts to the working solution. The presence of an aptamer could protect NB from such aggregation process due to its intercalation into double-stranded DNA and/or interaction with nucleobases. In response to the addition of the specific ligand, the competition between NB and the target for binding to the aptamer occurs, resulting in an increase in the dye salt aggregation and then in the blue-to-blank color change of the solution. The proof-of-principle was demonstrated by employing the anti-l-tyrosinamide aptamer and the assay was successfully applied to the trace enantiomer detection, allowing the detection of an enantiomeric impurity down to approximately 2% in a non-racemic sample. Through a reversed mechanism based on the increased capture of NB by DNA upon analyte binding, the sensing platform was further demonstrated for the Hg(II) detection. Water samples of different origin were spiked with Hg(II) analyte at final range concentrations comprised between (0.5-15 μM). An excellent overall recovery of 122 ± 14%; 105 ± 14%; 99 ± 9%; was respectively obtained from river, tap and mineral water, suggesting that the sensor can be used under real sample conditions. The assay was also shown to work for sensing the ochratoxin A and d-arginine vasopressin compounds, revealing its simplicity and generalizability potentialities.

Ultrasensitive hairpin mediated upconversion fluorescence biosensor for Staphylococcus aureus detection in foods and waters exploiting g-C3N4-assisted catalysis

A novel g-C₃N₄ nanosheets (g-C₃N₄ NSs)-assisted upconversion fluorescent aptasensor was proposed for Staphylococcus aureus (S. aureus) detection by adopting hybridization chain reaction (HCR) as a sensitizer. Two hairpin (H1 and H2) structured DNA probes were engineered predicated on the partial complementary sequence (cDNA) of S. aureus aptamer and modified on the exterior of the upconversion nanoparticles (UCNPs), respectively. The presence of S. aureus initiated the HCR system and activated H1 and H2 probes to form a double-helix away from the g-C₃N₄ NSs vicinity. This led to the decrease in peroxidase-like activity (PA) of the g-C₃N₄ NSs and corresponding fluorescence recovery proportional to the concentration of S. aureus (10-10⁶ cfu mL^-1). The method was applied to real food samples with acceptable recoveries (91.1-101.6%) and further validated by traditional plate counting method (p > 0.05).

A naphthalimide-tyrosine-based dicationic amphiphile for intracellular 'turn-on' simultaneous detection of ATP and CTP

We have developed a new naphthalimide-based amphiphile (YN-1) for the simultaneous detection of ATP and CTP. In YN-1, the cationic tyrosine-linked polyamine (+2 charge, hydrophilic unit) is appended at the -peri position of naphthalimide (hydrophobic unit). YN-1 and its Boc-protected compound 4 were characterized using state-of-the-art spectroscopic and optical techniques such as NMR, IR, UV-vis and fluorescence. The fluorescence data revealed that YN-1 showed a 'turn-on' (λ_em = 440 nm) fluorescence response for nanomolar detection of nucleoside triphosphates such as ATP and CTP in 20% HEPES buffer-DMSO solution. YN-1 also showed a concentration-based discrimination between ATP and CTP. YN-1 has been successfully applied for bioimaging of nucleoside triphosphates in MCF-7 live cancer cells with good compatibility. Therefore, the important findings from the present work will provide insight for future development of fluorescent probes to detect various kinds of essential nucleoside triphosphates.

Isolation of Bacteria Aptamers with Non-SELEX for the Development of a Highly Sensitive Colorimetric Assay Based on Dual Signal Amplification

In this work, an aptamer against Escherichia coli is isolated via non-SELEX, which executes efficient selection by employing repetitive cycles of centrifugation-based partitioning, and the binding site of the aptamer on E. coli cell surfaces is inferred to be a membrane protein. Moreover, truncated sequence 2-17-2 with a higher affinity (K_d = 101.76 nM) is employed for highly sensitive colorimetric detection of bacteria based on the dual signal amplification strategy. When targets exist, the release of DNA 1 from the polymer activates a hybridization chain reaction (HCR) between DNA 1 and DNA 2, thereby inducing the aggregation of probe 1. Subsequently, DNA 3 dissociated from probe 1 as a linker DNA further assembles probe 2/3. In this system, two types of DNA@gold nanoparticles (AuNPs) coexist and successively aggregate AuNPs based on divergent triggering mechanisms. Under optimal conditions, the dual signal amplification strategy presents excellent sensitivity (10 CFU mL^-1) and specificity, as well as the realization of real sample analysis.

A label-free aptasensor for the detection of ATP based on turn-on fluorescence DNA-templated silver nanoclusters

A label-free aptasensor has been fabricated in order to detect adenosine triphosphate (ATP) using turn-on fluorescence DNA-Ag NCs. The fluorescence of the DNA-Ag NCs could increase remarkably with the addition of ATP mainly because ATP specifically interacts with its aptamer to change the microenvironment of the darkish DNA-Ag NCs located at one terminus or two termini due to the conformational alteration of the aptamer structure. The proposed sensor can detect ATP in a linear range of 6-27 mM with a good detection limit of 5.0 μM. Additionally, the proposed method succeeded in detecting ATP in fetal bovine serum.

Plasma-assisted in-situ preparation of L-cystine functionalized silver nanoparticle: An intelligent multicolor nano-sensing of cadmium and paracetamol from environmental sample

L-cystine (L-cys) functionalized plasmonic silver nanomaterial (Ag NPs) was fabricated toward the selective and sensitive detection of paracetamol and cadmium. The prepared L-cys-Ag nanoparticles (NPs) were characterized by transmission electron microscopy (TEM), scanning electron microscopy (SEM), X-ray diffraction spectroscopy (XRD) and fourier transform infrared spectroscopy (FTIR) analyses. SEM imaging show that Ag NPs was decorated on the surface of L-cysteine 3D cubic nanosheet. L-cys-Ag NPs showed selective and sensitive detection towards paracetamol and cadmium. The interference study confirms that the presence of other metal ions didn't inhibit the detection of cadmium by L-cys-Ag NPs. The limit of detection of paracetamol and cadmium by L-cys-Ag NPs was calculated to be 1.2 and 2.82 nM respectively. In addition, the real sample detection of paracetamol on blood serum and urine, and cadmium on STP were performed and the recovery percentage was above 97%. Further, the real sample analysis was performed in tap and drinking water and the recovery percentage was more than 98%. The analytic logic gate on the multicolour detection of cadmium and paracetamol was performed for the semi-quantitative monitoring of paracetamol and cadmium by L-cys-Ag NPs. The developed L-cys-Ag NPs were found to be an effective tool for the monitoring of cadmium in environmental water bodies and paracetamol in blood and urine.

Dual-mode colorimetric-photothermal sensing platform of acetylcholinesterase activity based on the peroxidase-like activity of Fe-N-C nanozyme

Sensors based on colorimetry, fluorescence, and electrochemistry have been widely employed to detect acetylcholinesterase and its inhibitors, however, there are only a minority of strategies for AChE detection based on photothermal method. This work reports a versatile dual-mode colorimetric and photothermal biosensing platform for acetylcholinesterase (AChE) detection and its inhibitor (paraoxon-ethyl, a model of AChE inhibitors) monitor based on Fe-N-C/H₂O₂/3,3',5,5'-tetramethylbenzidine (TMB) system. The Fe-N-C with abundant active Fe-Nx sites shows outstanding peroxidase-mimicking activity and can be used to promote the generation of •OH by H₂O₂ to oxidize TMB. However, the introduction of mercapto molecules tending to coordinate with metal atoms result in the block of action site in Fe-N-C, thereby decrease its peroxidase-mimetic activity. The designed biosensor principle is based on the block of active sites of Fe-N-C by thiocholine (TCh, one kind of mercapto molecules) that can be produced by acetylthiocholine (ATCh) in the presence of AChE. Under optimum conditions, the limit of detection (LOD) for AChE activity is 1.9 mU mL^-1 (colorimetric) and 2.2 mU mL^-1 (photothermal), while for paraoxon-ethyl is 0.012 μg mL^-1 (colorimetric) and 0.013 μg mL^-1 (photothermal), respectively. The assay we proposed not only can be designed to monitor AChE detection and its inhibitors, but also can be easily extended for the detection of other biomolecules relate to the generation or consumption of H₂O₂.

Multimodal Ochratoxin A-Aptasensor Using 3'-FAM-Enhanced Exonuclease I Tool and Magnetic Microbead Carrier

Thanks to its preparatory ease, close affinity, and low cost, the aptasensor can serve as a promising substitute for antibody-dependent biosensors. However, the available aptasensors are mostly subject to a single-mode readout and the interference of unbound aptamers in solution and non-target-induced transition events. Herein, we proposed a multimodal aptasensor for multimode detection of ochratoxin A (OTA) with cross-validation using the 3'-6-carboxyfluorescein (FAM)-enhanced exonuclease I (Exo I) tool and magnetic microbead carrier. Specifically, the 3'-FAM-labeled aptamer/biotinylated-cDNA hybrids were immobilized onto streptavidin-magnetic microbeads via streptavidin-biotin interaction. With the presence of OTA, an antiparallel G-quadruplex conformation was formed, protecting the 3'-FAM labels from Exo I digestion, and then anti-FAM-horseradish peroxidase (HRP) was bound via specific antigen-antibody affinity; for the aptamers without the protection of OTA, the distal ssDNA was hydrolyzed from 3' → 5', releasing 3'-FAM labels to the solution. Therefore, the OTA was detected by analyzing the "signal-off" fluorescence of the supernatant and two "signal-on" signals in electrochemistry and colorimetry through the detection of the coating magnetic microbeads in HRP's substrate. The results showed that the 3'-FAM labels increased the activity of Exo I, producing a low background due to a more thorough digestion of unbound aptamers. The proposed multimodal aptasensor successfully detected the OTA in actual samples. This work first provides a novel strategy for the development of aptasensors with Exo I and 3'-FAM labels, broadening the application of aptamer in the multimode detection of small molecules.

Novel nitrogen-doped carbon dots for "turn-on" sensing of ATP based on aggregation induced emission enhancement effect

In this work, a nitrogen-doped carbon dots (CDs) was successfully synthesized by hydrothermal synthesis of polyethylenimine (PEI) and citric acid. The as-prepared CDs suffered from aggregation-caused quenching (ACQ) with a high concentration, but after adding adenosine triphosphate (ATP), the CDs aggregated. The generation of aggregates caused the rotation of the surface groups on CDs and reduced the non-radiation decay. The QY of CDs in water was 9.25 %, and increased to 16.60 % and 63.38% in the addition of 100 and 1000 μM ATP. And then, the enhancement of the radiation rate led to the aggregation induced enhancement effect (AIEE). Moreover, we also found that the proportion of precursors for CDs synthesis was a key factor in the occurrence of AIEE. Therefore, such CDs would be excellent candidates as fluorescent probes for the label-free detection of ATP. Our proposed method exhibited simple and easy preparation of nanoprobe, quick response (3 min), wide range of linear rage (1-2000 μM) and eco-friendly. In addition, the method performed successfully as a "turn-on" sensor for detection of ATP in the tablet with a recovery of 100.1~106.9% and RSD below 3.5%.

Highly sensitive detection of Tb3+ and ATP based on a novel asymmetric anthracene derivative

A novel fluorescent sensor based on an asymmetric anthracene derivative (SSAPA) was designed and synthesized. Using this molecule, a rapid and sensitive assay for detecting Tb³⁺ and ATP in aqueous solutions was established. The SSAPA molecule had excellent aggregation-induced emission (AIE) performance and good aqueous dispersion ability. This molecule could coordinate with Tb³⁺ and the fluorescence quenched linearly with the increase in the concentration of Tb³⁺ from 0.005 to 1.2 μM. Since both Tb³⁺ and adenosine triphosphate (ATP) have strong binding ability, ATP can compete with Tb³⁺ from the SSAPA/Tb³⁺ complex leading to fluorescence recovery. In this way, a brand-new fluorescent "turn-on" assay for ATP in the range from 0.01 to 0.4 μM was developed using the Tb³⁺-based complex probe. The detection limits for Tb³⁺ and ATP both reached single-digit nanomole per millilitre (2.8 nM and 4.5 nM, respectively), which demonstrated that this method has high sensitivity. Besides, Tb³⁺ and ATP also could be well detected in other complex environments such as real water samples or serum samples. This study provides a feasible assay for detecting trace amounts of Tb³⁺ and ATP in aqueous solutions.

Applications of hybridization chain reaction optical detection incorporating nanomaterials: A review

The development of powerful, simple and cost-effective signal amplifiers has significant implications for biological research and analysis. Hybridization chain reaction (HCR) has attracted increasing attention because of its enzyme-free, simple, and efficient amplification. In the HCR process, an initiator probe triggered a pair of metastable hairpins through a cross-opening process to propagate a chain reaction of hybridization events, yielding a long-nicked double-stranded nucleic acid structure. To achieve more noticeable signal amplification, nanomaterials, including graphene oxide, quantum dots, gold, silver, magnetic, and other nanoparticles, were integrated with HCR. Various types of colorimetric, fluorescence, plasmonic analyses or chemiluminescence optical sensing strategies incorporating nanomaterials have been developed to analyze various targets, such as nucleic acids, small biomolecules, proteins, and metal ions. This review summarized the recent advances of HCR technology pairing diverse nanomaterials in optical detection and discussed their challenges.

A robust colorimetric aptasensor for the label-free detection of marine toxins based on tyrosine-capped gold nanoparticles

Tyrosine-capped AuNPs decrease the interaction between targets and AuNPs, presenting better robustness than traditional Cit-AuNPs. Utilizing the superior features, a label-free aptasensor is developed for marine toxin detection for the first time.

A perylene diimide-based nanoring architecture for exogenous and endogenous ATP detection: biochemical assay for monitoring phosphorylation of glucose

Positively charged amphiphiles hold great significance in supramolecular chemistry due to their good solubility, and physiochemical and molecular recognition properties. Herein, we report the synthesis, characterization and molecular recognition properties of the dicationic amphiphile based on perylene diimide-tyrosine alkyl amide amine (PDI 3). PDI 3 showed the formation of a nanoring architecture in the self-assembled aggregated state (90% H₂O-DMSO mixture) as observed by SEM and TEM studies. The diameter of the nanoring is around 30-50 nm with a height varying from 1 to 2 nm. The self-assembled aggregates of PDI 3 are very sensitive towards nucleoside triphosphates. Upon addition of ATP, PDI 3 showed a decrease in the absorbance and emission intensity at 535 and 580 nm (due to the monomer state), respectively. The lowest detection limit for ATP is 10.8 nM (UV) and 3.06 nM (FI). Upon interaction of ATP with PDI 3, the nanoring morphology transformed into a spherical structure. These changes could be attributed to the formation of ionic self-assembled aggregates between dicationic PDI 3 and negatively charged ATP via electrostatic and H-bonding interactions. The complexation mechanism of PDI 3 and ATP was confirmed by optical, NMR, Job's plot, DLS, SEM and AFM studies. PDI 3 displays low cytotoxicity toward MG-63 cells and can be successfully used for the detection of exogenous and endogenous ATP. The resulting PDI 3 + ATP complex is successfully used as a 'turn-on' biochemical assay for monitoring phosphorylation of glucose.

Optimizing the hybridization chain reaction-fluorescence in situ hybridization (HCR-FISH) protocol for detection of microbes in sediments

Fluorescence in situ hybridization (FISH) is a canonical tool commonly used in environmental microbiology research to visualize targeted cells. However, the problems of low signal intensity and false-positive signals impede its widespread application. Alternatively, the signal intensity can be amplified by incorporating Hybridization Chain Reaction (HCR) with FISH, while the specificity can be improved through protocol modification and proper counterstaining. Here we optimized the HCR-FISH protocol for studying microbes in environmental samples, particularly marine sediments. Firstly, five sets of HCR initiator/amplifier pairs were tested on the laboratory-cultured bacterium Escherichia coli and the archaeon Methanococcoides methylutens, and two sets displayed high hybridization efficiency and specificity. Secondly, we tried to find the best combination of sample pretreatment methods and HCR-FISH protocol for environmental sample analysis with the aim of producing less false positive signals. Various detachment methods, extraction methods and formulas of hybridization buffer were tested using sediment samples. Thirdly, an image processing method was developed to enhance the DAPI signal of microbial cells against that of abiotic particles, providing a reliable reference for FISH imaging. In summary, our optimized HCR-FISH protocol showed promise to serve as an addendum to traditional FISH for research on environmental microbes.

Supplementary Information

The online version contains supplementary material available at 10.1007/s42995-021-00098-8.

A Pyrazolo Imine-based Colorimetric and Turn-on Fluorescent Sensor Probe for Determination of Hg2+ Ion and its Application in Test Paper Strips

In this work, we synthesized diethylamino substituted pyrazolo imine (3) fluorescent probe for recognition of Hg²⁺ ion.The sensor probe 3 can detect Hg²⁺ by colorimetric method, and there is a 10-fold enhancement in fluorescence response. When the fluorescent probe bound with Hg²⁺ ion, turn-on fluorescence was observed via the coordination. Probe 3 has an excellent selectivity toward Hg²⁺ in the CH₃ CN/H₂ O (8:2, v/v) solution with low limit of detection and high binding association constant of 551 parts per billion (ppb) and 6.6067 × 10⁶  m^-1 for 3+Hg²⁺ , respectively. Furthermore, the formation of 3+Hg²⁺ complex with 1:1 binding mode was evidenced by Job's plot, ¹ H NMR spectroscopy and Mass analysis. In addition, probe 3 is a feasible option to detect Hg²⁺ in various sources of water samples. Bio-imaging experiments have demonstrated that probe 3 can be used to monitor Hg²⁺ in Escherichia coli bacterial cell. The sensor 3 was also used for paper strip application to detect Hg²⁺ ion.

LSPR-based colorimetric biosensing for food quality and safety

Ensuring consistently high quality and safety is paramount to food producers and consumers alike. Wet chemistry and microbiological methods provide accurate results, but those methods are not conducive to rapid, onsite testing needs. Hence, many efforts have focused on rapid testing for food quality and safety, including the development of various biosensors. Herein, we focus on a group of biosensors, which provide visually recognizable colorimetric signals within minutes and can be used onsite. Although there are different ways to achieve visual color-change signals, we restrict our focus on sensors that exploit the localized surface plasmon resonance (LSPR) phenomenon of metal nanoparticles, primarily gold and silver nanoparticles. The typical approach in the design of LSPR biosensors is to conjugate biorecognition ligands on the surface of metal nanoparticles and allow the ligands to specifically recognize and bind the target analyte. This ligand-target binding reaction leads to a change in color of the test sample and a concomitant shift in the ultraviolet-visual absorption peak. Various designs applying this and other signal generation schemes are reviewed with an emphasis on those applied for evaluating factors that compromise the quality and safety of food and agricultural products. The LSPR-based colorimetric biosensing platform is a promising technology for enhancing food quality and safety. Aided by the advances in nanotechnology, this sensing technique lends itself easily for further development on field-deployable platforms such as smartphones for onsite and end-user applications.

Applications of scaffold-based advanced materials in biomedical sensing

There have been many efforts to synthesize advanced materials that are capable of real-time specific recognition of a molecular target, and allow the quantification of a variety of biomolecules. Scaffold materials have a porous structure, with a high surface area and their intrinsic nanocavities can accommodate cells and macromolecules. The three-dimensional structure (3D) of scaffolds serves not only as a fibrous structure for cell adhesion and growth in tissue engineering, but can also provide the controlled release of drugs and other molecules for biomedical applications. There has been a limited number of reports on the use of scaffold materials in biomedical sensing applications. This review highlights the potential of scaffold materials in the improvement of sensing platforms and summarizes the progress in the application of novel scaffold-based materials as sensor, and discusses their advantages and limitations. Furthermore, the influence of the scaffold materials on the monitoring of infectious diseases such as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and bacterial infections, was reviewed.

Integrating multiple hybridization chain reactions on gold nanoparticle and alkaline phosphatase-mediated in situ growth of gold nanobipyramids: An ultrasensitive and high color resolution colorimetric method to detect the mecA gene of Staphylococcus aureus

Colorimetry has been considered as a potential instrument-free platform for point-of-care genomic detection. However, it is limited by the poor sensitivity and low color resolution. Herein, we report a high-resolution colorimetric biosensor based on multiple hybridization chain reactions (HCRs) on gold nanoparticle (AuNP) and alkaline phosphatase (ALP)-mediated in situ growth of gold nanobipyramids (AuNBPs) for ultrasensitive detection of the Staphylococcus aureus (S. aureus) mecA gene. In our design, target DNA is hybridized with capture hairpin DNA on magnetic beads and then amplified by multiple HCRs on AuNP. Since biotin-labeled hairpin-structured nucleic acids are utilized to conduct HCRs, together with the large specific surface area of AuNP, the biotin- and streptavidin- based reaction results in a large amount of ALP on AuNP. With the aid of NADPH, ALP-mediated in situ growth of AuNBPs is observed, and a series of rainbow-like colors are associated with different target DNA concentrations. Through the multiple-amplification strategy produced by AuNP, HCRs, and enzymatic reactions, the target DNA as low as 2.71 pM can be detected with high specificity. Moreover, this method has been successfully applied to detect the mecA gene extracted from S. aureus. Therefore, the proposed method holds great potential in clinical diagnosis.

Electrochemical micro-aptasensors for exosome detection based on hybridization chain reaction amplification

Exosomes are cell-derived nanovesicles that have recently gained popularity as potential biomarkers in liquid biopsies due to the large amounts of molecular cargo they carry, such as nucleic acids and proteins. However, most existing exosome-based analytical sensing methods struggle to achieve high sensitivity and high selectivity simultaneously. In this work, we present an electrochemical micro-aptasensor for the highly sensitive detection of exosomes by integrating a micropatterned electrochemical aptasensor and a hybridization chain reaction (HCR) signal amplification method. Specifically, exosomes are enriched on CD63 aptamer-functionalized electrodes and then recognized by HCR products with avidin-horseradish peroxidase (HRP) attached using EpCAM aptamers as bridges. Subsequently, the current signal that is generated through the enzyme reaction between the HRP enzyme and 3,3',5,5'-tetramethylbenzidine (TMB)/H2O2 directly correlates to the amount of bound HRP on the HCR products and thus to the number of target exosomes. By introducing anti-EpCAM aptamers, micro-aptasensors can detect cancerous exosomes with high specificity. Due to the micropatterned electrodes and HCR dual-amplification strategy, the micro-aptasensors achieve a linear detection response for a wide range of exosome concentrations from 2.5×103 to 1×107 exosomes/mL, with a detection limit of 5×102 exosomes/mL. Moreover, our method successfully detects lung cancer exosomes in serum samples of early-stage and late-stage lung cancer patients, showcasing the great potential for early cancer diagnosis.

Advances in the Functional Nucleic Acid Biosensors for Detection of Lead Ions

Lead ions (Pb²⁺) are destructive to the natural environment and public health, so the efficient detection of Pb²⁺ is particularly important. Although the instrumental analysis methods have high accuracy, they require high cost and precise operation, which limits their wide application. Therefore, many strategies have been extensively studied for detecting Pb²⁺ by biosensors. Functional nucleic acids have become an efficient tool in this field. This review focuses on the recent biosensors of detecting Pb²⁺ based on functional nucleic acids from 2010 to 2020, in which DNAzyme, DNA G-quadruplex and aptamer will be introduced. The biosensors are divided into three categories that colorimetric, fluorometric and electrochemical biosensors according to the different reported signals. The action mechanism and detection effect of each biosensor are explained. Finally, the present situation of nucleic acid biosensor for the detection of Pb²⁺ is summarized and the future research direction is prospected.

Biosensors based on aptamer-conjugated gold nanoparticles: A review

Simply synthetized gold nanoparticles have been highly used in medicine and biotechnology as a result of their biocompatibility, conductivity, and being easily functionalized with biomolecules such as aptamer. Aptamer-conjugated gold nanoparticle structures synergically possess characteristics of both aptamer and gold nanoparticles including high binding affinity, high biocompatibility, enhanced target selectivity, and long circulatory half-life. Aptamer-conjugated gold nanoparticles have extensively gained considerable attention for designing of biosensing systems due to their interesting optical and electrochemical features. Moreover, biosensors based on aptamer-gold nanoparticles are easy to use, with fast response, and inexpensive which make them ideal in individualized medicine, disease markers detection, food safety, and so forth. Moreover, due to high selectivity and biocompatibility of aptamer-gold nanoparticles, these biosensing platforms are ideal tools for targeted drug delivery systems. The application of this nanostructure as diagnostic and therapeutic tool has been developed for detection of cancer in the early stage by detecting cancer biomarkers, pathogens, proteins, toxins, antibiotics, adenosine triphosphate, and other small molecules. This review obviously demonstrates that this nanostructure effectively is applicable in the field of biomedicine and possesses potential of commercialization aims.

Plasmon switching of gold nanoparticles through thermo-responsive terminal breathing of surface-grafted DNA in hydrated ionic liquids

Self-assembly performed in ionic liquids (ILs) as a unique solvent promises distinct functions and applications in sensors, therapeutics, and optoelectronic devices due to the rich interactions between nanoparticle building blocks and ILs. However, the general consideration that common nanoparticles are readily destabilized by counterions in an IL has largely prevented researchers from investigating controlled nanoparticle assembly in IL-based systems. This study explores the assembling behaviour of double-stranded (ds) DNA-functionalized gold nanoparticles (dsDNA-AuNPs) in hydrated ionic liquids. The DNA base pair stacking assembly of dsDNA-AuNPs occurs at a low IL concentration (<5%). However, a moderate ionic liquid concentration (5-40%) can de-hybridize dsDNA and leaves single-stranded (ss) DNA stabilizing the AuNPs. In concentrated ionic liquids (>40%), interestingly, the higher ionic strength leads to the assembly of DNA-AuNPs. The triphasic assembly trend is also generally observed regardless of the type of IL. By down-regulation of DNA's melting temperature with the IL, the assembly of DNA-AuNPs affords robust response to a lower temperature range, promising applications in plasmonic devices and range-tunable temperature sensors.

Development of a bioavailable Hg(II) sensing system based on MerR-regulated visual pigment biosynthesis

Engineered microorganisms have proven to be a highly effective and robust tool to specifically detect heavy metals in the environment. In this study, a highly specific pigment-based whole-cell biosensor has been investigated for the detection of bioavailable Hg(II) based on an artificial heavy metal resistance operon. The basic working principle of biosensors is based on the violacein biosynthesis under the control of mercury resistance (mer) promoter and mercury resistance regulator (MerR). Engineered biosensor cells have been demonstrated to selectively respond to Hg(II), and the specific response was not influenced by interfering metal ions. The response of violacein could be recognized by the naked eye, and the time required for the maximum response of violacein (5 h) was less than that of enhanced green fluorescence protein (eGFP) (8 h) in the single-signal output constructs. The response of violacein was almost unaffected by the eGFP in a double-promoter controlled dual-signals output construct. However, the response strength of eGFP was significantly decreased in this genetic construct. Exponentially growing violacein-based biosensor detected concentrations as low as 0.39 μM Hg(II) in a colorimetric method, and the linear relationship was observed in the concentration range of 0.78-12.5 μM. Non-growing biosensor cells responded to concentrations as low as 0.006 μM Hg(II) in a colorimetric method and in a Hg(II) containing plate sensitive assay, and the linear relationship was demonstrated in a very narrow concentration range. The developed biosensor was finally validated for the detection of spiked bioavailable Hg(II) in environmental water samples.

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.

Gold based nano-photonic approach for point-of-care detection of circulating long non-coding RNAs

Development of a rapid, sensitive and easy to use point of care assay for detection of circulating long non-coding RNAs (lncRNAs) is of great importance. These biomolecules possess the ability to regulate vital cellular processes and act as biomarkers for various human non-communicable diseases. The present work aimed to develop a simplified and reliable cytometric fluorescence-based approach for precise recognition of circulating lncRNAs in a given sample using biotinylated uracil-modified oligonucleotide tethered AlexaFluor488-labeled streptavidin gold colloidal (BiO-StrAG) nano-conjugates. The fluorophores in close proximity to the gold nanoparticles result in quenching of fluorescence; however, specific recognition of target lncRNAs increases this distance which causes plasmonic enhancement of fluorescence. As per the flow cytometry and fluorometry investigations, the developed methodology provides a precise and sensitive approach for detection of the target lncRNAs (up to 5 nM in any given sample). With advantages of high selectivity and feasibility, our strategy offers great potential of being developed as a promising tool for interrogating aberrant regulation of lncRNAs functions, especially indicated in various diseased states.

Techniques for Detection of Clinical Used Heparins

Heparins and sulfated polysaccharides have been recognized as effective clinical anticoagulants for several decades. Heparins exhibit heterogeneity depending on the sources. Meanwhile, the adverse effect in the clinical uses and the adulteration of oversulfated chondroitin sulfate (OSCS) in heparins develop additional attention to analyze the purity of heparins. This review starts with the description of the classification, anticoagulant mechanism, clinical application of heparins and focuses on the existing methods of heparin analysis and detection including traditional detection methods, as well as new methods using fluorescence or gold nanomaterials as probes. The in-depth understanding of these techniques for the analysis of heparins will lay a foundation for the further development of novel methods for the detection of heparins.

Novel perylene probe-encapsulated metal-organic framework nanocomposites for ratiometric fluorescence detection of ATP

Adenosine triphosphate (ATP) plays an important role in various biological processes and the ATP level is closely associated with many diseases. Herein, a novel ratiometric fluorescence assay for ATP was developed based on the excimer-monomer transfer of a perylene probe. By encapsulating a perylene probe, N,N'-bis(6-caproic acid)-3,4:9,10-perylenediimide (PDI), into zeolitic imidazolate framework-8 (ZIF-8) nanocrystals, fluorescent nanocomposites (PDI@ZIF-8) with significant excimer emission of the perylene probe were prepared for the first time. The presence of ATP will trigger the decomposition of PDI@ZIF-8 due to much stronger coordination between ATP and Zn2+ than that of 2-methylimidazole and Zn2+. As a result, the encapsulated PDI probes were released, leading to significantly increased monomer emission accompanying the decrease in the excimer emission. The excimer-monomer transition signal was utilized for ratiometric ATP sensing and its potential application for detecting ATP in cell lysates was also successfully demonstrated.

A sensitive electrochemiluminescence DNA biosensor based on the signal amplification of ExoIII enzyme-assisted hybridization chain reaction combined with nanoparticle-loaded multiple probes

An electrochemiluminescence (ECL) DNA biosensor based on ExoIII exonuclease assistance and hybridization chain reaction (HCR) amplification technology has been constructed. ExoIII exonuclease and triple-helix DNA molecular switch are used in detecting a target in circulation. By combining HCR with AuNPs@DNA, a novel signal probe is built, which enables multiple signal amplification and the high-sensitive detection of transgenic rice BT63 DNA. The Fe₃O₄@Au solution is added to a magneto-controlled glassy carbon electrode, and sulfhydryl-modified capture DNA (CP) is immobilized on Fe₃O₄@Au through the Au-S bond. Mercaptoethanol is added to close sites and prevent the nonspecific adsorption of CP on the magnetron glassy carbon electrode. A target DNA is added to a constructed triple-helix DNA molecular centrifuge tube for reaction. Owing to base complementation and the reversible switching of the triple-helix DNA molecular state, the target DNA turns on the triple-helix DNA molecular switch and hybridizes with a long-strand recognition probe (RP) to form a double-stranded DNA (dsDNA). Exonuclease ExoIII is added to specifically recognize and cut the dsDNA and to release the target DNA. The target DNA strand then circulates back completely to open the multiple triple-helix DNA molecular switch, releasing a large number of signal transduction probes (STP). To hybridize with CP, a large amount of STP is added to the electrode. Finally, a AuNPs@DNA signal probe is added to hybridize with STP. H1 and H2 probes are added for the hybridization chain reaction and the indefinite extension of the primer strand on the probe. Then, tris-(bipyridyl)ruthenium(II) is added for ECL signal detection with PBS-tri-n-propylamine as the base solution. In the concentration range 1.0 × 10^-16 to 1.0 × 10^-8 mol/L of the target DNA, good linear relationship was achieved with the corresponding ECL signal. The detection limit is 3.6 × 10^-17 mol/L. The spiked recovery of the rice samples range from 97.2 to 101.5%. The sensor is highly sensitive and has good selectivity, stability, and reproducibility. A novel electrochemiluminescence biosensor with extremely higher sensitivity was prepared for the determination of ultra-trace amount transgenic rice BT63 DNA. The sensitivity was significantly improved by multiple signal enhancements. Firstly, a large number of signal transduction probes are released when the triple-helix DNA molecular switch unlock after recycles assisted by ExoIII exonuclease under target BT63 DNA; and then the signal transduction probes hybridize with the signal probes of AuNPs@(DNA-HCR) produced through hybridization chain reaction. Finally, the signal probes which were embedded with a large amount of electrochemiluminescence reagent produce high luminescence intensity. The detection limit was 3.6 × 10^-17 mol/L, which is almost the most sensitive methods reported.

Aptasensors for mycotoxin detection: A review

Mycotoxins are toxic compounds produced by fungi, which represent a risk to the food and feed supply chain, having an impact on health and economies. A high percentage of feed samples have been reported to be contaminated with more than one type of mycotoxin. Systematic, cost-effective and simple tools for testing are critical to achieve a rapid and accurate screening of food and feed quality. In this review, we describe the various aptamers that have been selected against mycotoxins and their incorporation into optical and electrochemical aptasensors, outlining the strategies exploited, highlighting the advantages and disadvantages of each approach. The review also discusses the different materials used and the immobilization methods employed, with the aim of achieving the highest sensitivity and selectivity.

Colorimetric Detection of Class A Soybean Saponins by G-Quadruplex-Based Hybridization Chain Reaction

Soybean saponin is one of the important secondary metabolites in seeds, which has various beneficial physiological functions to human health. GmSg-1 gene is the key enzyme gene for synthesizing class A saponins. It is of great significance to realize the visual and rapid detection of class A saponins at the genetic level. The hybridization chain reaction (HCR) was employed to the visual detection of GmSg-1 gene, which was implemented by changing the length of the target fragment to 92 bp and using the hairpin probes we designed to detect the GmSg-1 ^a and GmSg-1 ^b genes. The best condition of HCR reaction is hemin (1.2 μM), Triton X-100 (0.002%), ABTS (3.8 μM), and H₂O₂ (1.5 mM). It was found that HCR has high specificity for GmSg-1 gene and could be applied to the visual detection of different soybean cultivars containing Aa type, Ab type, and Aa/Ab type saponins, which could provide technical reference and theoretical basis for molecular breeding of soybean and development of functional soybean products.

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.

A Critical Factor for Quantifying Proteins in Unmodified Gold Nanoparticles-Based Aptasensing: The Effect of pH

Unmodified gold nanoparticles (AuNPs)-based aptasensing (uGA) assay has been widely implemented in the determination of many different targets, but there are few reports on protein detection using uGA. Here, we designed a uGA assay for protein detection including the elimination of interfering proteins. Positively charged protein can be absorbed directly on the surface of AuNPs to form “protein corona”, which results in the aggregation of AuNPs even without salt addition, thereby preventing target protein detection. To overcome this problem, we systematically investigated the effect of modifying the pH of the solution during the uGA assay. A probe solution with a pH slightly higher than the isoelectric points (pI) of the target protein was optimal for protein detection in the uGA assay, allowing the aptamer to selectively detect the target protein. Three proteins (beta-lactoglobulin, lactoferrin, and lysozyme) with different pI were chosen as model proteins to validate our method. Positively charged interfering proteins (with pIs higher than the optimal pH) were removed by centrifugation of protein corona/AuNPs aggregates before the implementation of actual sample detection. Most importantly, the limit of detection (LOD) for all three model proteins was comparable to that of other methods, indicating the significance of modulating the pH. Moreover, choosing a suitable pH for a particular target protein was validated as a universal method, which is significant for developing a novel, simple, cost-effective uGA assay for protein detection.