Hairpin DNA as a Biobarcode Modified on Gold Nanoparticles for Electrochemical DNA Detection

DNA nanoassembly based turn-on amplification probe for sensitive colorimetric CRISPR/Cas12a-mediated detection of pathogen DNA

Clustered regularly interspaced short palindromic repeat (CRISPR) system has been explored as an efficient tool for nucleic acid diagnostics. However, it normally needs instrumentation or produces turn-off signals. Herein, a bulged Y-shape DNA (Y-DNA) nanoassembly was designed and synthesized as a novel turn-on probe. A CRISPR/Cas12a and Y-DNA probe mediated colorimetric assay (named as CYMCOA) strategy was developed for visual detection of pathogen DNA. Upon activating Cas12a with pathogen DNA, the Y-DNA bulge is catalytically trans-cleaved, releasing the G-quadruplex sequence embedded in the Y-DNA nanoassembly as a peroxidase-like DNAzyme. Visible signals with chromogen substrates are thus produced. The CYMCOA strategy was combined with recombinase polymerase amplification (RPA), an isothermal amplification technique, in detecting Helicobacter pylori (Hp) bacteria and SARS-CoV-2 N plasmids as two model pathogens. The bioassay has very excellent detection sensitivity and specificity, owing to the triple cascade amplification reactions and the very low mismatch tolerance. The lower limit of detection values were 0.16 cfu⋅mL-1, 1.5 copies⋅μL-1, and 0.17 copies⋅μL-1 for Hp bacteria, Hp plasmids, and SARS-CoV-2 N plasmids respectively. The detection is fast and accurate. The colorimetric bioassay strategy provides to be a simple, accurate, fast and instrumentation-free platform for nucleic acids detections in various settings, including crude and emergent situations.

A double methylene blue labeled single-stranded DNA and hairpin DNA coupling biosensor for the detection of Fusarium oxysporum f. sp. cubense race 4

The DCL gene in Fusarium oxysporum f. sp. cubense Race 4 (Foc4) is a pivotal pathogenic factor causing banana fusarium wilt. Precise DCL detection is crucial for Foc4 containment. Here, we present a novel ssDNA-hDNA coupling electrochemical biosensor for highly specific DCL detection. The sensing interface was formed via electrodeposition of a composite containing reduced graphene oxide (rGO) and gold nanoparticles (AuNPs) onto a carbon screen-printed electrode (SPE), followed by thiol-modified ssDNA functionalization. Additionally, the incorporation of hDNA, with methylene blue (MB) at both ends, binds to ssDNA through base complementarity, forming an ssDNA-hDNA coupling probe with bismethylene blue. This sensing strategy relies on DCL recognition by the hDNA probe, leading to DNA hairpin unfolding and detachment of hDNA bearing two MBs from ssDNA, generating a robust "on-off" signal. Empirical results demonstrate the sensor's amplified electrical signals, reduced background currents, and an extended detection range (6.02 × 106-3.01 × 1010 copies/μL) with a limit of detection (3.01 × 106 copies/μL) for DCL identification. We applied this sensor to analyze soil, banana leaves, and fruit samples, confirming its high specificity and stability. Moreover, post-sample detection, the sensor exhibits reusability, offering a cost-effective and rapid approach for banana wilt detection.

Advances on diagnosis of Helicobacter pylori infections

The association of Helicobacter pylori to several gastric diseases, such as chronic gastritis, peptic ulcer disease, and gastric cancer, and its high prevalence worldwide, raised the necessity to use methods for a proper and fast diagnosis and monitoring the pathogen eradication. Available diagnostic methods can be classified as invasive or non-invasive, and the selection of the best relies on the clinical condition of the patient, as well as on the sensitivity, specificity, and accessibility of the diagnostic test. This review summarises all diagnostic methods currently available, including the invasive methods: endoscopy, histology, culture, and molecular methods, and the rapid urease test (RUT), as well as the non-invasive methods urea breath test (UBT), serological assays, biosensors, and microfluidic devices and the stool antigen test (SAT). Moreover, it lists the diagnostic advantages and limitations, as well as the main advances for each methodology. In the end, research on the development of new diagnostic methods, such as bacteriophage-based H. pylori diagnostic tools, is also discussed.

Nucleic Acid Based Testing (NABing): A Game Changer Technology for Public Health

Timely and accurate detection of the causal agent of a disease is crucial to restrict suffering and save lives. Mere symptoms are often not enough to detect the root cause of the disease. Better diagnostics applied for screening at a population level and sensitive detection assays remain the crucial component of disease surveillance which may include clinical, plant, and environmental samples, including wastewater. The recent advances in genome sequencing, nucleic acid amplification, and detection methods have revolutionized nucleic acid-based testing (NABing) and screening assays. A typical NABing assay consists of three modules: isolation of the nucleic acid from the collected sample, identification of the target sequence, and final reading the target with the help of a signal, which may be in the form of color, fluorescence, etc. Here, we review current NABing assays covering the different aspects of all three modules. We also describe the frequently used target amplification or signal amplification procedures along with the variety of applications of this fast-evolving technology and challenges in implementation of NABing in the context of disease management especially in low-resource settings.

Aptamer-based technology for gastric cancer theranostics

Gastric cancer is one of the most common causes of cancer death worldwide. This cancer exhibits high molecular and phenotype heterogeneity. The overall survival rate for gastric cancer is very low because it is always diagnosed in the advanced stages. Therefore, early detection and treatment are of great significance. Currently, biomedical studies have tapped the potential clinical applicability of aptamer-based technology for gastric cancer diagnosis and targeted therapy. Herein, we summarize the enrichment and evolution of relevant aptamers, followed by documentation of the recent developments in aptamer-based techniques for early diagnosis and precision therapy for gastric cancers.

Integration of DNA barcoding and nanotechnology in drug delivery

In recent years' development in nanotechnology utilization of DNA barcodes with potential benefit of nanoparticulate system is a hallmark for novel advancement in healthcare, biomedical and research sector. Interplay of biological barcoding with nanodimensional system encompasses innovative technologies to offer unique advantages of ultra-sensitivity, error-free, accuracy with minimal label reagents, and less time consumption in comparison to conventional techniques like ELISA, PCR, culture media, electrophoresis. DNA barcoding systems used as universal novel tool for identification and multiplex structural detection of proteins, DNAs, toxins, allergens, and nucleic acids of humans, viruses, animals, bacteria, plants as well as personalized treatment in ovarian cancer, AIDS-related Kaposi sarcoma, breast cancer and cardiovascular diseases. Barcoding tools offer substantial attention in drug delivery, in-vivo screening, gene transport for theranostics, bioimaging, and nano-biosensors applications. This review article outlines the recent advances in nano-mediated DNA barcodes to explore various applications in detection of cancer markers, tumor cells, pathogens, allergens, as theranostics, biological sensors, and plant authentication. Furthermore, it summarizes the diverse newer technologies such as bio-barcode amplification (BBA), Profiling Relative Inhibition Simultaneously in Mixtures (PRISM) and CRISPR-Cas9 gene knockout and their applications as sensors for detections of antigens, allergens, and other specimens.

Advanced Sensing Strategies Based on Different Types of Biomarkers toward Early Diagnosis of H. pylori

Helicobacter pylori (H. pylori) is a bacterium that can colonize human gastric epithelial cells and cause H. pylori infection, closely related to many gastric diseases. Compared with conventional H. pylori detection methods, emerging diagnostic approaches (such as biosensors) have become potentially more effective alternatives due to their high sensitivity, good selectivity and noninvasiveness. This review begins with a brief overview of H. pylori infection, the processes that lead to diseases, and current diagnostic methods. Subsequently, advanced biosensors in different target-based for diagnosing H. pylori infection are focused, including the detection of H. pylori-related nucleic acid, H. pylori-related protein (such as the cytotoxin, urease), and intact H. pylori. In addition, prospects for the development of H. pylori detection methods are also discussed in the end.

Three-Dimensional Surface-Enhanced Raman Scattering Platform with Hotspots Built by a Nano-mower for Rapid Detection of MRSA

Methicillin-resistant Staphylococcus aureus (MRSA) has become one of the greatest threats to human health due to its strong drug resistance, wide distribution range, and high infection rate. Rapid identification of MRSA strains is very important for accurate diagnosis and early treatment of MRSA infections. Here, we introduced an Exo III-assisted nanomotor mower to build 3D hotspots for rapid detection of MRSA by surface-enhanced Raman scattering (SERS). As the bacteria bound to the aptamer, two trigger chains were released from the double-stranded structure, and the nano-mowers were activated by opening a hairpin probe on gold nanoparticles (AuNPs). With the continued cleavage of Exo III and cyclic release of the trigger chain, multiple hairpin DNAs on the AuNPs were cleaved to increase the motor power. The resulting nano-mower continued slicing protective DNA from larger AuNPs, exposing the AuNPs. Without the protection of DNA, Mg²⁺ in the buffer induced spontaneous aggregation of the AuNPs, and a large number of hotspots were formed for SERS measurements. Under optimal conditions, MRSA can be detected within 40 min, and the concentration of MRSA showed a good linear relationship with the SERS intensity at 1342 cm^-1, with a limit of detection as low as 1 CFU/mL and a wide linear range (10⁰ to 10⁷ CFU/mL). This strategy creates a rapid bacterial detection method that performs well on actual samples utilizing portable Raman spectroscopy instruments, with potential applications in food detection, water detection, clinical treatment, and diagnosis.

Stabilization of Gold Nanoparticles by Hairpin DNA and Implications for Label-Free Colorimetric Biosensors

With extremely high extinction coefficients and other unique optical properties, gold nanoparticles (AuNPs) have received growing interest in developing biosensors. DNA hairpin structures are very popular probes for the detection of not only complementary DNA or RNA but also aptamer targets. This work aims to understand the effect of the structure and sequence of hairpin DNA for the stabilization of AuNPs and its implications in AuNP-based label-free colorimetric biosensors. A series of hairpin DNA with various loop sizes from 4 to 26 bases and sequences (random sequences, poly-A and poly-T) were tested, but they showed similar abilities to protect AuNPs from aggregation. Using hairpin DNA with a tail under the same conditions, optimal protection was achieved with a six-base or longer tail. DNA hairpins are likely adsorbed via their tail regions or with their terminal bases if no tail is present. Molecular dynamics simulations showed that the rigidity of the hairpin loop region disfavored its adsorption to AuNPs, while the flexible tail region is favored. Finally, a DNA sensing assay was conducted using different structured DNA, where hairpin DNA with a tail doubled the sensitivity compared to the tail-free hairpin.

Ratiometric electrochemical aptasensor for the sensitive detection of carcinoembryonic antigen based on a hairpin DNA probe and exonuclease I-assisted target recycling

A novel ratiometric electrochemical aptasensor was constructed for the detection of carcinoembryonic antigen (CEA) based on a hairpin DNA (hpDNA) probe and exonuclease Ⅰ (Exo Ⅰ)-assisted target recycling amplification strategy. A thiolated methylene blue (MB)-labeled hpDNA as the internal control element was fixed on the surface of the gold nanoparticles (AuNPs)-modified gold electrode (AuE) through Au-S bonds. A ferrocene (Fc)-modified aptamer DNA (Fc-Apt) was partially hybridized with hpDNA to form a Fc-Apt/hpDNA duplex. Due to the specific recognition of Fc-Apt to CEA, the presence of CEA caused dissociation of Fc-Apt from the duplex, and further triggered the degradation process of Exo Ⅰ and recycling of CEA. Hence, the Fc tags were released from the electrode surface and the oxidation peak current of Fc (I_Fc) decreased while that of MB (I_MB) remained stable owing to the distance between MB tags and the electrode unchanged. A linear relationship was observed between I_Fc/I_MB and the logarithm of CEA concentration from 10 pg mL^-1 to 100 ng mL^-1 with a detection limit of 1.9 pg mL^-1. Moreover, the developed aptasensor had been applied to detect CEA in diluted human serum with satisfactory results, indicating its great potential in practical applications.

An ultrasensitive biosensor for prostate specific antigen detection in complex serum based on functional signal amplifier and designed peptides with both antifouling and recognizing capabilities

The development of biosensors capable of averting biofouling and detecting biomarkers in complex biological media remains a challenge. Herein, an ultralow fouling and highly sensitive biosensor based on specifically designed antifouling peptides and a signal amplification strategy was designed for prostate specific antigen (PSA) detection in human serum. A low fouling layer of poly(ethylene glycol) (PEG) doped the conducting polymer poly(3,4-ethylenedioxythiophene) (PEDOT) was electrodeposited on the electrode surface, followed by the immobilization of streptavidin and further attachment of biotin-labelled peptides. The peptide was designed to include PSA specific recognition domain (HSSKLQK) and antifouling domain (PPPPEKEKEKE), and the terminal of the peptide was functionalized with -SH group. DNA functionalized gold nanorods (DNA/AuNRs) were then attached to the electrode, and methylene blue (MB) molecules were adsorbed to the DNA to form the signal amplifier. In the presence of PSA, the peptide was specifically cleaved and resulted in the loss of AuNRs together with DNA and MB, and thus significant decrease of the current signal. The biosensor exhibited a low limit of detection (LOD) of 0.035 pg mL^-1 (S/N = 3), with a wide linear range from 0.10 pg mL^-1 to 10.0 ng mL^-1, and it was able to detect PSA in real human serum owing to the presence of the antifouling peptides, indicating great potential of the constructed biosensor for practical application.

Fabrication strategies and surface tuning of hierarchical gold nanostructures for electrochemical detection and removal of toxic pollutants

The intensive research on the synthesis and characterization of gold (Au) nanostructures has been extensively documented over the last decades. These investigations allow the researchers to understand the relationships between the intrinsic properties of Au nanostructures such as particle size, shape, morphology, and composition to synthesize the Au nano/hybrid nanostructures with novel physicochemical properties. By tuning the properties above, these nanostructures are extensively employed to detect and remove trace amounts of toxic pollutants from the environment. This review attempts to document the achievements and current progress in Au-based nanostructures, general synthetic and fabrication strategies and their utilization in electrochemical sensing and environmental remediation applications. Additionally, the applications of Au nanostructures (e.g., as adsorbents, sensing platforms, catalysts, and electrodes) and advancements in the field of electrochemical sensing of different target analytes (e.g., proteins, nucleic acids, heavy metals, small molecules, and antigens) are summarized. The literature survey concludes the existing methods for the detection of toxic contaminants at various concentration levels. Finally, the existing challenges and future research directions on electrochemical sensing and degradation of toxic contaminants using Au nanostructures are defined.

Advances in diagnosis of Helicobacter pylori through biosensors: Point of care devices

Invasive as well as non-invasive conventional techniques for the detection of Helicobacter pylori (H. pylori) have several limitations that are being overcome by the development of novel, rapid and reliable biosensors. Herein, we describe several biosensors fabricated for the detection of H. pylori. This review aims to provide the principles of biosensors and their components including in the context to H. pylori detection. The major biorecognition elements in H. pylori detection include antigen/antibodies, oligonucleotides and enzymes. Furthermore, the review describes the transducers, such as electrochemical, optical and piezoelectric, also including microfluidics approaches. An overview of the biomarkers associated with H. pylori pathogenesis is also discussed. Finally, the prospects of advancement and commercialization of point-of-care tools are summarized.

A sensitive electrochemical DNA sensor for detecting Helicobacter pylori based on accordion-like Ti3C2Tx: a simple strategy

A novel electrochemical DNA sensor was designed to detect Helicobacter pylori based on accordion-like Ti₃C₂T_x. Here the multilayer Ti₃C₂T_x obtained by DMSO delamination was used to modify the glass carbon electrode, with a large specific surface area and excellent conductivity. Au nanoparticles were supported on the modified electrode and worked as an effective carrier to fix the capture probe (cpDNA) with sulfhydryl group through the firm binding of Au-S bond. Such an accordion-like Ti₃C₂T_x structure provides an ultrahigh electroactive surface area and ample binding sites for accommodating Au nanoparticles, which is advantageous for the signal amplification during the detection. And further, the sandwich structure formed by hybridizing cpDNA with target DNA sequence (tDNA) and rpDNA (rpDNA is a strand of DNA that can be base-paired with the tested tDNA) increases greatly the current signal and enhances the sensitivity of the electrochemical DNA sensor. Under optimal conditions, the developed electrochemical DNA sensor showed a wide linear range from 10^-11 to 10^-14 M and a low detection limit of 1.6 × 10^-16 M and exhibited good sensitivity, reproducibility, and stability. A novel electrochemical DNA sensor with simple sandwich structure was designed to detect H. pylori based on accordion-like Ti₃C₂T_x.

Preparation, Functionalization, Modification, and Applications of Nanostructured Gold: A Critical Review

Gold nanoparticles (Au NPs) play a significant role in science and technology because of their unique size, shape, properties and broad range of potential applications. This review focuses on the various approaches employed for the synthesis, modification and functionalization of nanostructured Au. The potential catalytic applications and their enhancement upon modification of Au nanostructures have also been discussed in detail. The present analysis also offers brief summaries of the major Au nanomaterials synthetic procedures, such as hydrothermal, solvothermal, sol-gel, direct oxidation, chemical vapor deposition, sonochemical deposition, electrochemical deposition, microwave and laser pyrolysis. Among the various strategies used for improving the catalytic performance of nanostructured Au, the modification and functionalization of nanostructured Au produced better results. Therefore, various synthesis, modification and functionalization methods employed for better catalytic outcomes of nanostructured Au have been summarized in this review.

DNA Nanoswitch Barcodes for Multiplexed Biomarker Profiling

Molecular biomarkers play a key role in the clinic, aiding in diagnostics and prognostics, and in the research laboratory, contributing to our basic understanding of diseases. Detecting multiple and diverse molecular biomarkers within a single accessible assay would have great utility, providing a more comprehensive picture for clinical evaluation and research, but is a challenge with standard methods. Here, we report programmable DNA nanoswitches for multiplexed detection of up to 6 biomarkers at once with each combination of biomarkers producing a unique barcode signature among 64 possibilities. As a defining feature of our method, we show "mixed multiplexing" for simultaneous barcoded detection of different types of biomolecules, for example, DNA, RNA, antibody, and protein in a single assay. To demonstrate clinical potential, we show multiplexed detection of a prostate cancer biomarker panel in serum that includes two microRNA sequences and prostate specific antigen.

Silver or gold? A comparison of nanoparticle modified electrochemical genosensors based on cobalt porphyrin-DNA

We applied a cobalt-porphyrin modified DNA as electrochemical marker, which was attached to nanoparticles, to detect specific DNA sequences. We compare the performance of gold and silver NPs in oligonucleotide sensors to determine if a change in metal will lead to either higher sensitivity or different selectivity, based on the redox behaviour of silver vs. gold. Surprisingly, we find that using either gold or silver NPs yields very similar overall performance. The electrochemical measurements of both types of sensors show the same redox behaviour which is dominated by the cobalt porphyrin, indicating that the electron pathway does not include the NP, but there is direct electron transfer between the porphyrin and the electrode. Both sensors show a linear response in the range of 5 × 10^-17-1 × 10^-16 M; the limit of detection (LOD) is 3.8 × 10^-18 M for the AuNP sensor, and 5.0 × 10^-18 M for the AgNP sensor, respectively, which corresponds to the detection of about 20-50 DNA molecules in the analyte. Overall, the silver system results in a better DNA economy and using cheaper starting materials for the NPs, thus shows better cost-effectivness and could be more suitable for the mass-production of highly sensitive DNA sensors.

Three-Dimensional DNA Nanomachine Biosensor by Integrating DNA Walker and Rolling Machine Cascade Amplification for Ultrasensitive Detection of Cancer-Related Gene

Stochastic DNA walkers capable of traversing on three-dimensional (3D) tracks have received great deal of attention. However, DNA walker-based biosensors exhibit limited amplification efficiency because of their slow walking kinetics and low processivity. Herein, by taking advantage of the high processivity of a DNA rolling machine, a sensitive ratiometric DNA nanomachine biosensor is designed. The biosensor is constructed with hairpin-loaded Au nanoparticles (NPs) (hpDNA@AuNPs) as a DNA walker and AgNCs-decorated magnetic NPs (AgNCs@MNPs) as a DNA rolling machine. In the presence of target DNA, exonuclease III (Exo III)-powered DNA walker is activated to accomplish first-stage amplification via a burnt-bridge mechanism, generating a great deal of toehold-loaded AuNPs (Toehold@AuNPs) to hybridize with magnetic nanoparticles loaded with silver-nanoclusters-labeled DNA (AgNCs@MNPs) with the assistance of Exo III. These trigger rapid rolling of AuNPs on the AgNCs@MNPs surface and release free AgNCs, converting the biological signal into a mass spectrometric signal ratio (¹⁰⁷Ag/¹⁹⁷Au) with detection by ICP-MS. A linear range of 0.5-500 fmol L^-1 is achieved with a detection limit of 119 amol L^-1 for the p53 gene. The practical applicability of the biosensor has been demonstrated in the accurate assay of the p53 gene in the human blood.

Discrimination of narcotic drugs in human urine based on nanoplasmonics combined with chemometric method

The detection of psychoactive substances is an important branch of modern analytical chemistry and has many legally and socially relevant implications. The use of a surface plasmon resonance (SPR)-based gene-nanoparticle system has emerged as a promising technique for the rapid and ultrasensitive detection of molecular species such as drugs of abuse in biofluids. However, the development of a viable screening tool for the detection of multiple classes of drugs in complex media is a considerable challenge because the existing techniques lack affinity toward certain species due to matrix interference. Our aim was to develop a simple optical sensor array for the classification of nine narcotic drugs in aqueous solution and human urine. The UV-vis spectra of DNA-gold nanoparticles in the presence of nine narcotic drugs (pentobarbital sodium, caffeine, morphine, remifentanil, fentanyl, ketamine, etomidate, carfentanil, and sulfentanyl) were distinctly different. Furthermore, the narcotic drugs present in aqueous solution and in human urine were classified correctly through partial least squares discriminant analysis (PLS-DA). Combination with a multi-sensor unit further improved the prediction accuracy of the PLS-DA models. The proposed method has potential for on-site drug detection and drug abuse screening.

An enzyme-free electrochemical sandwich DNA assay based on the use of hybridization chain reaction and gold nanoparticles: application to the determination of the DNA of Helicobacter pylori

An ultrasensitive enzyme-free electrochemical sandwich DNA biosensor is described for the detection of ssDNA oligonucleotides. A DNA sequence derived from the genom of Helicobacter pylori was selected as a model target DNA. The DNA assay was realized through catching target DNA on capture DNA immobilized gold electrode; then labeling the target DNA with reporter DNA (rpDNA) and initiator DNA (iDNA) co-modified gold nanoparticles (AuNPs). The high density of iDNAs serves as one of the amplification strategies. The iDNA triggers hybridization chain reaction (HCR) between two hairpins. This leads to the formation of a long dsDNA concatamer strand and represents one amplification strategy. The electrochemical probe [Ru(NH₃)₅L]²⁺, where L stands for 3-(2-phenanthren-9-ylvinyl)pyridine, intercalated into dsDNA chain. Multiple probe molecules intercalate into one dsDNA chain, serving as one amplification strategy. The electrode was subjected to differential pulse voltammetry for signal acquisition, and the oxidation peak current at -0.28 V was recorded. On each AuNP, 240 iDNA and 25 rpDNA molecules were immobilized. Successful execution of HCR at the DNA-modified AuNPs was confirmed by gel electrophoresis and hydrodynamic diameter measurements. Introduction of HCR significantly enhances the DNA detection signal intensity. The assay has two linear ranges of different slopes, one from 0.01 fM to 0.5 fM; and one from 1 fM to 100 fM. The detection limit is as low as 0.68 aM. Single mismatch DNA can be differentiated from the fully complementary DNA. Conceivably, this highly sensitive and selective assay provides a general method for detection of various kinds of DNA. Graphical abstractSchematic representation of the detection and the amplification principles of the electrochemical sandwich DNA assay. Purple curl: Captured DNA; Green curl: Reporter DNA; Orange curl: HCR initiator DNA; Yellow solid-circle: Gold nanoparticle; H1 and H2: Two hairpin DNA; [Ru(NH₃)₅L]²⁺: Signal probe.

Bio-barcode detection technology and its research applications: A review

With the rapid development of nanotechnology, the bio-barcode assay (BCA), as a new diagnostic tool, has been gradually applied to the detection of protein and nucleic acid targets and small-molecule compounds. BCA has the advantages of high sensitivity, short detection time, simple operation, low cost, good repeatability and good linear relationship between detection results. However, bio-barcode technology is not yet fully formed as a complete detection system, and the detection process in all aspects and stages is unstable. Therefore, studying the optimal reaction conditions, optimizing the experimental steps, exploring the multi-residue detection of small-molecule substances, and preparing immuno-bio-barcode kits are important research directions for the standardization and commercialization of BCA. The main theme of this review was to describe the principle of BCA, provide a comparison of its application, and introduce the single-residue and multi-residue detection of macromolecules and single-residue detection of small molecules. We also compared it with other detection methods, summarized its feasibility and limitations, expecting that with further improvement and development, the technique can be more widely used in the field of stable small-molecule and multi-residue detection.

Label-free and amplified electrogenerated chemiluminescence biosensing for the detection of thymine DNA glycosylase activity using DNA-functionalized gold nanoparticles triggered hybridization chain reaction

Effective detection of thymine DNA glycosylase (TDG) activity is extremely crucial and urgent for epigenetic research. Herein, a novel label-free electrogenerated chemiluminescence (ECL) biosensing method was developed for the detection of TDG activity using DNA-functionalized gold nanoparticles (DNA-AuNPs) triggered hybridization chain reaction (HCR). In this assay, the thiol modified hairpin probe DNA (hp-DNA) with 5' overhangs and one mismatched base pair of guanines: thymine (G: T) in the stem part was boned onto gold electrode. TDG specifically removed T base of the G: T mismatch to produce apyrimidinic (AP) sites through the N-glycosidic bond hydrolysis. The AP site was then cleaved by the catalysis of Endonuclease IV (EnIV) to generate dsDNA containing a free 3' end in the long sequence, which serves as a complementary sequence to hybridize with the specific sequence (ssDNA1) of DNA-AuNPs. Then, the functionalized DNA-AuNPs with initiator strands (ssDNA2) could trigger HCR to form nicked double helices DNA polymer which can embed numerous ECL indicator, Ru(phen)₃²⁺, resulting in significantly increased ECL signal. The proposed strategy combined the amplification function of DNA-AuNPs triggered HCR and the inherent high sensitivity of the ECL technique, a detection limit of 1.1 × 10^-5 U/μL (0.0028 ng/mL) for TDG determination was obtained. In addition, this method was successfully applied to evaluate TDG activity in cancer cell, which provides great possibility for TDG activity assay in related clinical diagnostics.

Neutral Charged Immunosensor Platform for Protein-based Biomarker Analysis with Enhanced Sensitivity

A noninvasive, highly sensitive universal immunosensor platform for protein-based biomarker detection is described in this Article. A neutral charged sensing environment is constructed by an antibody with an oppositely charged amino acid as surface charge neutralizer. By adjusting the pH condition of the testing environment, this neutral charged immunosensor (NCI) directly utilizes the electrostatic charges of the analyte for quantification of circulating protein markers, achieving a wide dynamic range covering through the whole picomole level. Comparing with previous studies on electrostatic charges characterization, this NCI demonstrates its capability to analyze not only the negatively charged biomolecules but also positively charged analytes. We applied this NCI for the detection of HE4 antigen with a detection limit at 2.5 pM and Tau antigen with a detection limit at 0.968 pM, demonstrating the high-sensitivity property of this platform. Furthermore, this NCI possesses a simple fabrication method (less than 2 h) and a short testing turnaround time (less than 30 min), providing an excellent potential for further clinical point-of-care applications.

Sensor array for qualitative and quantitative analysis of metal ions and metal oxyanion based on colorimetric and chemometric methods

Gold nanoparticle (AuNP)-based colorimetric sensor is sensitive for the detection of metal ions and metal oxyanion in aqueous solution. However, this method is usually not suitable for multi-objective analysis in complex mixture systems because it is suffering from interference of co-existents. In the present paper, we proposed a sensitive, flexible, low-cost, and multi-units sensor method for the qualitative and quantitative analysis of metal ions and metal oxyanion based on the global ultraviolet and visible (UV-Vis) spectra of amino acid-gold nanoparticles (amino acid-AuNPs) sensors in the range of 230-800 nm. Different amino acids (L-Histidine, L-Lysine, L-Methionine, D-Penicillium) which can prevent the aggregation of the AuNPs in NaCl solution, were investigated to build sensor arrays responding to different ions induced AuNPs aggregation. The UV-Vis spectra that Cd²⁺, Ba²⁺, Mn²⁺, Ni²⁺, Cu²⁺, Fe³⁺, Cr³⁺, Cr₂O₇^2-, Sn⁴⁺, Pb²⁺ induce amino acid-AuNPs displayed different characteristics and the ions were classified correctly by using partial least squares-discriminant analysis (PLS-DA). Taking the advantage of the multivariate analysis and sensor arrays, we simultaneously quantified the ions in binary and ternary mixture systems (Cr³⁺/Cr₂O₇^2-, Fe³⁺/Cd²⁺, Fe³⁺/Cr³⁺/Cr₂O₇^2-). Data fusion methods further improved the prediction accuracy of the chemometric models built on multi-amino acids-AuNPs sensors. The proposed method has a potential for analyzing metal ions and metal oxyanion in much more complex mixture systems.

Colorimetric chiral recognition of D/L-phenylalanine based on triangular silver nanoplates

A new colorimetric analysis approach for chiral recognition of D- and L-forms of phenylalanine (phe) was developed based on triangular silver nanoplates (TAg-NPs). The TAg-NPs could be used as chiral colorimetric probes for D- and L-forms of phe. Upon addition of D-phe to TAg-NPs solution, a color change from blue to purple to pink could be observed, while no obvious color change was found on addition of L-phe. L-phe could prevent the TAg-NPs from being etched to small size particles while the protective effect of D-phe was weak. Moreover, the enantiomeric excess of D-phe could be determined using the proposed chiral assay in the percentage of L-phe from 0 to 100% with a correlation coefficient of 0.9855. The phenomenon could be monitored by bare eyes and quantified analysis by UV-Vis spectrophotometry. The developed approach had several advantages, such as simplicity, visualization, short analysis time and low cost. This study presented a fast visualization analysis method of chiral D/L-phenylalanine and may lay the foundation for the development of visualization chiral recognition of other target analytes.

High-performance electrochemical sensing of circulating tumor DNA in peripheral blood based on poly-xanthurenic acid functionalized MoS2 nanosheets

A high-performance sensing platform based on poly-xanthurenic acid (PXA) film functionalized MoS₂ nanosheets was developed for electrochemical detection of circulating tumor DNA in peripheral blood. The MoS₂ nanosheets were obtained using a simple ultrasonic method from bulk MoS₂. The physical adsorption between MoS₂ and aromatic XA monomers effectively improved the electropolymerization efficiency, accompanied with an increased electrochemical response of PXA. The obtained PXA/MoS₂ nanocomposite not only served as a substrate for DNA immobilization but also reflected the electrochemical transduction originating from DNA immobilization and hybridization without any complex labelling processes or outer indicators. The immobilization of the probe ssDNA was achieved via noncovalent assembly due to the π-π interaction between PXA and DNA bases. After the hybridization of the probe ssDNA with the target DNA, the formation of helix structure induced the resulted dsDNA to be released from the surface of the PXA/MoS₂ nanocomposite. The detection limit of this constructed DNA biosensor was calculated in the linear target DNA concentrations range from 1.0 × 10^-16 mol/L to 1.0 × 10^-10 mol/L and it was found to be 1.8 × 10^-17 mol/L.

Approaching single DNA molecule detection with an ultrasensitive electrochemical genosensor based on gold nanoparticles and cobalt-porphyrin DNA conjugates

An ultrasensitive genosensor is obtained by using gold nanoparticles and cobalt-porphyrin labelled DNA reporter strands with an attomolar detection limit.

Detection of Helicobacter pylori in dental plaque using a DNA biosensor for noninvasive diagnosis

H. pylori in dental plaque was detected with a DNA biosensor with results correlating well with the ¹³C urea breath test.

Ultrasensitive detection of nucleic acids based on dually enhanced fluorescence polarization

Increase of the molecular volume and quenching effect induced by AuNP conjugation can both enhance the fluorescence polarization of Alexa488.

Beta-Hemolytic Bacteria Selectively Trigger Liposome Lysis, Enabling Rapid and Accurate Pathogen Detection

For more than a century, blood agar plates have been the only test for beta-hemolysis. Although blood agar cultures are highly predictive for bacterial pathogens, they are too slow to yield actionable information. Here, we show that beta-hemolytic pathogens are able to lyse and release fluorophores encapsulated in sterically stabilized liposomes whereas alpha and gamma-hemolytic bacteria have no effect. By analyzing fluorescence kinetics, beta-hemolytic colonies cultured on agar could be distinguished in real time with 100% accuracy within 6 h. Additionally, end point analysis based on fluorescence intensity and machine-extracted textural features could discriminate between beta-hemolytic and cocultured control colonies with 99% accuracy. In broth cultures, beta-hemolytic bacteria were detectable in under an hour while control bacteria remained negative even the next day. This strategy, called beta-hemolysis triggered-release assay (BETA) has the potential to enable the same-day detection of beta-hemolysis with single-cell sensitivity and high accuracy.

Electroactive crown ester-Cu2+ complex with in-situ modification at molecular beacon probe serving as a facile electrochemical DNA biosensor for the detection of CaMV 35s

A novel electrochemical DNA biosensor has been facilely constructed by in-situ assembly of electroactive 4'-aminobenzo-18-crown-6-copper(II) complex (AbC-Cu2+) on the free terminal of the hairpin-structured molecule beacon. The 3'-SH modified molecule beacon probe was first immobilized on the gold electrode (AuE) surface through self-assembly chemistry of Au-S bond. Then the crow ester of AbC was covalently coupled with 5'-COOH on the molecule beacon, and served as a platform to attach the Cu2+ by coordination with ether bond (-O-) of the crown cycle. Thus, an electroactive molecule beacon-based biosensing interface was constructed. In comparison with conventional methods for preparation of electroactive molecule beacon, the approach presented in this work is much simpler, reagent- and labor-saving. Selectivity study shows that the in-situ fabricated electroactive molecule beacon remains excellent recognition ability of pristine molecule beacon probe to well differentiate various DNA fragments. The target DNA can be quantatively determined over the range from 0.10pM to 0.50nM. The detection limit of 0.060pM was estimated based on signal-to-noise ratio of 3. When the biosensor was applied for the detection cauliflower mosaic virus 35s (CaMV 35s) in soybean extraction samples, satisfactory results are achieved. This work opens a new strategy for facilely fabricating electrochemical sensing interface, which also shows great potential in aptasensor and immurosensor fabrication.