Enhanced electrochemical recognition of double-stranded DNA by using hybridization chain reaction and positively charged gold nanoparticles

Triblock polyadenine-based electrochemical aptasensor for ultra-sensitive detection of carcinoembryonic antigen via exonuclease III-assisted target recycling and hybridization chain reaction

Carcinoembryonic antigen (CEA), a key colon biomarker, demands a precise detection method for cancer diagnosis and prognosis. This study introduces a novel electrochemical aptasensor using a triblock polyadenine probe for ultra-sensitive detection of CEA. The method leverages Exonuclease III (Exo III)-assisted target recycling and hybridization chain reaction. The triblock polyadenine probe self-assembles on the bare gold electrode through the strong affinity between adenine and gold electrode, blocking CEA diffusion and providing a large immobilization surface. CEA binding to hairpin probe 1 (HP1), followed by the hybridization between HP1 and hairpin probe 2 (HP2), triggers DNA cleavage by Exo III, amplifying the signal via a hybridization chain reaction and producing numerous dsDNA walkers that generates a dramatic electrochemical impedance signal. Under optimized conditions, the aptasensor achieved two ultra-low detection limits: 0.39 ag∙mL-1 within the concentration range of 5 ag∙mL-1 to 5 × 106 ag∙mL-1, and 1.5 ag∙mL-1 within the concentration range of 5 × 106 ag∙mL-1 to 1 × 1010 ag∙mL-1. Its performance in human serum samples meets the practical standards, offering a promising new tool for ultrasensitive tumor marker detection, potentially revolutionizing early cancer diagnosis.

Rapid ultra-sensitive nucleic acid detection using plasmonic fiber-optic spectral combs and gold nanoparticle-tagged targets

Nucleic acid (NA) is a widely-used biomarker for viruses. Accurate quantification of NA can provide a reliable basis for point-of-care diagnosis and treatment. Here, we propose a tilted fiber Bragg grating (TFBG)-based plasmonic fiber-optic spectral comb for fast response and ultralow limit NA detection. The TFBG is coated with a gold film which enables excitation of surface plasmon resonance (SPR), and single-stranded probe NAs with known base sequences are assembled on the gold film. To enhance sensitivity of refractive index (RI) for sensing a chosen combination of probe and target NAs around the TFBG surface, gold nanoparticles (AuNPs) are bonded to the target NA molecules as "RI-labels". The NA combination-induced aggregation of AuNPs induces significant spectral responses in the TFBG that would be below the detection threshold for the NAs in the absence of the AuNPs. The proposed TFBG-SPR NA sensor shows a fast response time of 30 s and an ultra-wide NA detection range from 1 × 10-18 mol/L to 1 × 10-7 mol/L. In the NA concentration range of 1 × 10-12 mol/L (1 pM) to 105 pM, an ultra-high sensitivity of 1.534 dB/lg(pM) is obtained. The sensor achieves an ultra-low limit of detection down to 1.0 × 10-18 mol/L (1 aM), which is more than an order of magnitude lower than the previous reports. The proposed sensor not only shows potentials in practical applications of NA detection, but also provides a new way for TFBG-SPR biochemical sensors to achieve higher RI sensitivity.

Rose bengal-mediated photoinduced atom transfer radical polymerization for high sensitivity detection of target DNA

Convenient and sensitive detection of biomolecules is of utmost importance in the field of early disease screening. In this study, a Rose Bengal-Mediated photoinduced atom transfer radical polymerization (photoATRP) method was used to achieve highly sensitive detection of target DNA (tDNA). The tDNA was specifically recognized using PNA with terminal modified sulfhydryl groups, and the initiator α-bromophenylacetic acid (BPAA) was attached to the electrode surface via a phosphate-Zr⁴⁺-carboxylate acid structure. Under the excitation of blue light, rose bengal (RB) acts as a photocatalyst, β-nicotinamide adenine dinucleotide (NADH) as an electron donor, and ferrocenylmethyl methacrylate (FMMA) as a monomer to activate the photoATRP reaction and generate a large number of electroactive polymer chains on the electrode surface. Under optimal conditions, the method can be used for the quantitative analysis of tDNA in the concentration range of 1-10⁵ fM (R² = 0.994) with a limit of detection (LOD) of 0.115 fM. This metal-free mediated photoATRP biosensor, with low cost and environmental friendliness, has great potential in the field of highly sensitive biomolecule detection.

Applications of triplex DNA nanostructures in sensor development

Triplex DNA nanostructures are one of the most emerging and fascinating self-assembled nanostructures due to their unique nanoparticle-like organization and inherit characteristics. They have attracted numerous interests recently because of their versatile and powerful utility in diverse areas of science and technology, such as clinical or disease diagnosis and stimuli-based drug delivery. This review addresses particularly the utilization of DNA triplexes in the development of biosensors for detecting nucleic acid; strategies in sensing pH, protein activity, ions, or molecules. Finally, an outlook for potential applications of triplex DNA nanoswitches is provided.

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.

Electrochemical Sensor for Directional Recognition and Measurement of Antibiotic Resistance Genes in Water

The establishment of rapid targeted identification and analysis of antibiotic resistance genes (ARGs) is very important. In this study, an electrochemical sensor, which can detect ARGs was obtained by modifying the sulfhydryl single-stranded DNA probe onto the thin-film gold electrode through self-assembly. The sensor can perform a hybridization reaction with a target sequence to obtain an electrochemical impedance spectroscopy signal. The results showed that when the concentration of the probe used to modify thin-film gold electrodes during preparation was 1 μM, the hybridization time was 1 h, and the hybridization temperature was 35 °C, the self-assembled sensor showed good detection performance for the ARGs encoding β-lactam hydrolase. The measurement ARG concentration linear range is 6.3-900.0 ng/mL, and the R² is 0.9992. The sensor shows good specific recognition ability for single-base, double-base, and three-base mismatch DNA. In addition, after 30 days of storage at 4 °C, the accurate identification and analysis of ARGs can still be maintained.

In Situ Assembly of Nanomaterials and Molecules for the Signal Enhancement of Electrochemical Biosensors

The physiochemical properties of nanomaterials have a close relationship with their status in solution. As a result of its better simplicity than that of pre-assembled aggregates, the in situ assembly of nanomaterials has been integrated into the design of electrochemical biosensors for the signal output and amplification. In this review, we highlight the significant progress in the in situ assembly of nanomaterials as the nanolabels for enhancing the performances of electrochemical biosensors. The works are discussed based on the difference in the interactions for the assembly of nanomaterials, including DNA hybridization, metal ion-ligand coordination, metal-thiol and boronate ester interactions, aptamer-target binding, electrostatic attraction, and streptavidin (SA)-biotin conjugate. We further expand the range of the assembly units from nanomaterials to small organic molecules and biomolecules, which endow the signal-amplified strategies with more potential applications.

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.

Implications of the Coffee-Ring Effect on Virus Infectivity

The factors contributing to the survival of enveloped viruses (e.g., influenza and SARS-CoV-2) on fomite surfaces are of societal interest. The bacteriophage Phi6 is an enveloped viral surrogate commonly used to study viability. To investigate how viability changes during the evaporation of droplets on polypropylene, we conducted experiments using a fixed initial Phi6 concentration while systematically varying the culture concentration and composition (by amendment with 2% fetal bovine serum (FBS), 0.08 wt % BSA, or 0.5 wt % SDS). The results were consistent with the well-founded relative humidity (RH) effect on virus viability; however, the measured viability change was greater than that previously reported for droplets containing either inorganic salts or proteins alone, and the protein effects diverged in 1× Dulbecco's modified Eagle's medium (DMEM). We attribute this discrepancy to changes in virus distribution during droplet evaporation that arise due to the variable solute drying patterns (i.e., the "coffee-ring" effect) that are a function of the droplet biochemical composition. To test this hypothesis, we used surface-enhanced Raman spectroscopy (SERS) imaging and three types of gold nanoparticles (pH nanoprobe, positively charged (AuNPs(+)), and negatively charged (AuNPs(-))) as physical surrogates for Phi6 and determined that lower DMEM concentrations, as well as lower protein concentrations, suppressed the coffee-ring effect. This result was observed irrespective of particle surface charge. The trends in the coffee-ring effect correlate well with the measured changes in virus infectivity. The correlation suggests that conditions resulting in more concentrated coffee rings provide protective effects against inactivation when viruses and proteins aggregate.

An electrochemical biosensor based on a graphene oxide modified pencil graphite electrode for direct detection and discrimination of double-stranded DNA sequences

The ability to directly recognize double-stranded DNA (ds-DNA) is a major challenge in disease diagnosis and gene therapy because DNA is naturally double-stranded. Herein, a novel electrochemical biosensor for the sequence-specific recognition of ds-DNA using a peptide nucleic acid (PNA) probe and graphene oxide (GO) modified pencil graphite electrode is reported and applied for the direct detection of the desired sequence in plasmid samples. For this purpose, GO was assembled onto the pencil graphite electrode surface (GO/PGE) by a simple casting method and applied for PNA probe immobilization (PNA-GO/PGE). Upon addition of ds-DNA, the interaction of the PNA probe with ds-DNA induces probe detachment from the electrode surface which results in a guanine oxidation signal decrease. Under optimized conditions, the guanine oxidation signal decreased linearly with the ds-DNA concentration increasing in the range from 30 pM to 10 nM, with a detection limit of 1.3 pM. Moreover, the proposed biosensor was applied for the sensitive and selective detection of double-stranded target DNA in plasmid samples. This proposed method could be used as a platform for direct detection of various sequences in double-stranded genomic DNA.

A simple and rapid colorimetric detection of serum lncRNA biomarkers for diagnosis of pancreatic cancer

A colorimetric assay is developed for detection of lncRNA HOTTIP by one-step reverse transcription-loop-mediated isothermal amplification (RT-LAMP) coupled with positively-charged gold nanoparticles ((+)AuNP) for diagnosis of pancreatic cancer. This assay allows simple, rapid, and sensitive quantification of lncRNA down to 50 copies.

Dual signal amplification by polysaccharide and eATRP for ultrasensitive detection of CYFRA 21-1 DNA

Cytokeratin fragment antigen 21-1 (CYFRA 21-1) DNA is a crucial biomarker closely associated with non-small cell lung cancer. Here, we fabricated a novel electrochemical biosensor for ultrasensitive detection of CYFRA 21-1 DNA via polysaccharide and electrochemically mediated atom transfer radical polymerization (eATRP) dual signal amplification. Specifically, thiolated peptide nucleic acid (PNA) probes at 5'-terminals are immobilized on the gold electrode surface for specific recognition of CYFRA 21-1 DNA (tDNA). After hybridization, hyaluronic acid (HA) is linked to the hybridized PNA/DNA duplexes via the recognized carboxylate-Zr⁴⁺-phosphate chemistry. Then multiple initiators of the polymerization reaction are introduced via esterification reaction. Lastly, large numbers of electro-active monomers are successfully grafted from the initiation sites of functionalized HA by eATRP reaction, significantly amplifying the electrochemical signal. Under optimal conditions, the constructed sensor can detect as low as 9.04 aM tDNA. Further, this proposed biosensor can also be applied to the direct detection of double-stranded DNA (dsDNA), obtaining 0.12 fM as the detection limit. Besides, this strategy shows high selectivity for mismatched bases and excellent applicability for CYFRA 21-1 DNA detection in the serum samples. Given its high sensitivity, selectivity, ease of operation, low cost and environmental friendliness, this biosensor has considerable potential in early diagnosis and biomedical application.

Non-invasive diagnosis of bladder cancer by detecting telomerase activity in human urine using hybridization chain reaction and dynamic light scattering

Cystoscopy and histology are the gold standards for detection of bladder cancer. However, these methods are highly subjective, expensive, and invasive. We have developed a non-invasive method for the diagnosis of bladder cancer by detecting telomerase activity in human urine. Telomerase substrate (TS) primer is elongated with repeating sequences of (TTAGGG)n in the presence of telomerase. The elongated primer can trigger hybridization chain reaction between two hairpins H1 and H2, result in the aggregation of AuNPs due to the hybridization between the tail sequence on H1 (or H2) and DNA-AuNPs probe, and accompany with the increase of hydrodynamic diameter of AuNPs, which can be measured with dynamic light scattering (DLS). The biosensor displayed a detection limit of 4 MCF-7 cells (a signal-to-noise ratio of 3) and a dynamic range of 10-1000 cells. Moreover, only urine specimens from bladder cancer patients induced a significant change in the average hydrodynamic diameter, indicating its specificity for the non-invasive diagnosis of bladder cancer.

Experimental and theoretical investigation for surface plasmon resonance biosensor based on graphene/Au film/D-POF

A D-shape plastic optical fiber (D-POF) surface plasmon resonance (SPR) biosensor based on the graphene/Au film (G/Au) was proposed and experimentally demonstrated for detection of DNA hybridization process. To improve the detection performance of SPR sensors, the Physical Vapor Deposition (PVD) method was used to evaporate the Au film directly onto the graphene grown on copper foil, and the Au film acted as a role of traditional Polymethyl Methacrylate (PMMA). The process made graphene and Au film form seamless contact. Next, the G/Au was transferred onto the D-shape fiber together. We explored the G/Au SPR sensor by using the finite element method (FEM) and obtained the optimum materials thickness to form configuration. Compared to other plastic optical fiber experiments, the proposed sensor's sensitivity was improved effectively and calculated as 1227 nm/RIU in a range of glucose solution. Meanwhile, our proposed sensor successfully distinguishes hybridization and single nucleotide polymorphisms (SNP) by observing the resonance wavelength change. It also exhibits a satisfactory linear response (R² = 0.996) to the target DNA liquids with respective concentrations of 0.1nM to1µM, which shows this method's wide potential in medical diagnostics.

Sensitive fluorometric determination of platelet-derived growth factor BB and avian influenza A virus DNA via dual signal amplification using the hybridization chain reaction and glucose oxidase assisted recycling

A method is described for fluorometric determination of platelet-derived growth factor BB (PDGF-BB) and avian influenza A (H1N1) virus DNA. It is based on the use of the hybridization chain reaction (HCR) and of glucose oxidase (GOx) assisted dual-recycling amplification. A silver coated glass slide (SCGS) serves as an ideal material for separation. A signal DNA/initiator triggers the HCR and generates a cascade of hybridization to form a nicked double-helix polymer. Upon addition of the analytes (PDGF-BB or H1N1 DNA) and capture DNA immobilized on the SCGS, the nicked double-helix polymer binds on the surface of the SCGS through formation of a [capture DNA/analyte/signal DNA] sandwich structure. The GOx-biotin-streptavidin (SA) complexes were then attached to the nicked double-helix polymer through SA-biotin interaction. After cleavage by DNase I, the bound GOx is transferred into the buffer. Glucose is added and enzymatically oxidized to produce H₂O₂. The H₂O₂ formed oxidizes the substrate 3-(p-hydroxyphenyl)-propanoic acid to give a blue fluorescent product (with excitation/emission maxima at 320/416 nm) under the catalysis of horseradish peroxidase. Under optimal conditions, fluorescence increases linearly in the 0.5 to 70 pmol·L^-1 PDGF-BB concentration range, and the detection limit is 191 fmol·L^-1. For the H1N1 virus DNA, the respective data are 2.5 to 300 pmol·L^-1 and 826 fmol·L^-1. Graphical abstract Schematic presentation for detection of analytes (PDGF-BB or H1N1 virus DNA) based on the dual-signal amplification of Hybridization Chain Reaction (HCR) and glucose oxidase (GOx) using silver coated glass slide (SCGS) as separation material.

Liquid biopsy of circulating tumor DNA and biosensor applications

Circulating tumor DNA (ctDNA) as a class of liquid biopsy is a type of gene fragment that contains tumor-specific gene changes in body fluids such as human peripheral blood. More and more evidences show that ctDNA is an excellent tumor biomarker for diagnosis, prognosis, tumor heterogeneity and so on. ctDNA is a tumor code in the blood. Liquid biopsy of ctDNA is firstly summarized. Compared with the traditional detection technologies of ctDNA, the biosensor is an excellent choice for the detection of ctDNA because of its portability, sensitivity, specificity and ease of use. This review mainly evaluates various biosensors applied to the detection of ctDNA. We discuss the most commonly used bioreceptors to specifically identify and bind ctDNA, including complementary DNA (cDNA), peptide nucleic acid (PNA) and anti-5 MethylCytosines, and the biotransducers which convert biological signals to analysable signs. The review also discusses signal amplification strategies in biosensors to detect ctDNA.

Development of an Electrochemical DNA Biosensor to Detect a Foodborne Pathogen

Vibrio parahaemolyticus (V. parahaemolyticus) is a common foodborne pathogen that contributes to a large proportion of public health problems globally, significantly affecting the rate of human mortality and morbidity. Conventional methods for the detection of V. parahaemolyticus such as culture-based methods, immunological assays, and molecular-based methods require complicated sample handling and are time-consuming, tedious, and costly. Recently, biosensors have proven to be a promising and comprehensive detection method with the advantages of fast detection, cost-effectiveness, and practicality. This research focuses on developing a rapid method of detecting V. parahaemolyticus with high selectivity and sensitivity using the principles of DNA hybridization. In the work, characterization of synthesized polylactic acid-stabilized gold nanoparticles (PLA-AuNPs) was achieved using X-ray Diffraction (XRD), Ultraviolet-visible Spectroscopy (UV-Vis), Transmission Electron Microscopy (TEM), Field-emission Scanning Electron Microscopy (FESEM), and Cyclic Voltammetry (CV). We also carried out further testing of stability, sensitivity, and reproducibility of the PLA-AuNPs. We found that the PLA-AuNPs formed a sound structure of stabilized nanoparticles in aqueous solution. We also observed that the sensitivity improved as a result of the smaller charge transfer resistance (Rct) value and an increase of active surface area (0.41 cm²). The development of our DNA biosensor was based on modification of a screen-printed carbon electrode (SPCE) with PLA-AuNPs and using methylene blue (MB) as the redox indicator. We assessed the immobilization and hybridization events by differential pulse voltammetry (DPV). We found that complementary, non-complementary, and mismatched oligonucleotides were specifically distinguished by the fabricated biosensor. It also showed reliably sensitive detection in cross-reactivity studies against various food-borne pathogens and in the identification of V. parahaemolyticus in fresh cockles.

Chemical and Biological Sensing Using Hybridization Chain Reaction

Since the advent of its theoretical discovery more than 30 years ago, DNA nanotechnology has been used in a plethora of diverse applications in both the fundamental and applied sciences. The recent prominence of DNA-based technologies in the scientific community is largely due to the programmable features stored in its nucleobase composition and sequence, which allow it to assemble into highly advanced structures. DNA nanoassemblies are also highly controllable due to the precision of natural and artificial base-pairing, which can be manipulated by pH, temperature, metal ions, and solvent types. This programmability and molecular-level control have allowed scientists to create and utilize DNA nanostructures in one, two, and three dimensions (1D, 2D, and 3D). Initially, these 2D and 3D DNA lattices and shapes attracted a broad scientific audience because they are fundamentally captivating and structurally elegant; however, transforming these conceptual architectural blueprints into functional materials is essential for further advancements in the DNA nanotechnology field. Herein, the chemical and biological sensing applications of a 1D DNA self-assembly process known as hybridization chain reaction (HCR) are reviewed. HCR is a one-dimensional (1D) double stranded (ds) DNA assembly process initiated only in the presence of a specific short ssDNA (initiator) and two kinetically trapped DNA hairpin structures. HCR is considered an enzyme-free isothermal amplification process, which shows substantial promise and offers a wide range of applications for in situ chemical and biological sensing. Due to its modular nature, HCR can be programmed to activate only in the presence of highly specific biological and/or chemical stimuli. HCR can also be combined with different types of molecular reporters and detection approaches for various analytical readouts. While the long dsDNA HCR product may not be as structurally attractive as the 2D and 3D DNA networks, HCR is highly instrumental for applied biological, chemical, and environmental sciences, and has therefore been studied to foster a variety of objectives. In this review, we have focused on nucleic acid, protein, metabolite, and heavy metal ion detection using this 1D DNA nanotechnology via fluorescence, electrochemical, and nanoparticle-based methodologies.

Triplex DNA Nanostructures: From Basic Properties to Applications

Triplex nucleic acids have recently attracted interest as part of the rich "toolbox" of structures used to develop DNA-based nanostructures and materials. This Review addresses the use of DNA triplexes to assemble sensing platforms and molecular switches. Furthermore, the pH-induced, switchable assembly and dissociation of triplex-DNA-bridged nanostructures are presented. Specifically, the aggregation/deaggregation of nanoparticles, the reversible oligomerization of origami tiles and DNA circles, and the use of triplex DNA structures as functional units for the assembly of pH-responsive systems and materials are described. Examples include semiconductor-loaded DNA-stabilized microcapsules, DNA-functionalized dye-loaded metal-organic frameworks (MOFs), and the pH-induced release of the loads. Furthermore, the design of stimuli-responsive DNA-based hydrogels undergoing reversible pH-induced hydrogel-to-solution transitions using triplex nucleic acids is introduced, and the use of triplex DNA to assemble shape-memory hydrogels is discussed. An outlook for possible future applications of triplex nucleic acids is also provided.

Electrochemically mediated in situ growth of electroactive polymers for highly sensitive detection of double-stranded DNA without sequence-preference

The ability to directly detect double-stranded DNA (dsDNA) without sequence-preference continues to be a major challenge. Herein, we report an electrochemical method for the direct, highly sensitive detection of dsDNA based on the strand replacement of dsDNA by peptide nucleic acid (PNA) and the in situ growth of electroactive polymers through the surface-initiated electrochemically mediated atom transfer radical polymerization (SI-eATRP). Thiolated PNA molecules are firstly self-assembled onto gold electrode surface for the specific recognition of target dsDNA (dsDNA-T), which in turn leads to the formation of a high density of PNA/DNA heteroduplexes on the electrode surface for the subsequent attachment of ATRP initiators via the phosphate-Zr⁴⁺-carboxylate chemistry. By applying a negative potential to the electrode, the air-stable Cu^II deactivators can be reduced into the Cu^I activators so as to trigger the surface-initiated polymerization for the in situ growth of electroactive polymers. Due to the strand replacement of dsDNA by PNA, dsDNA can be directly detected without sequence-preference. Besides, the growth of polymers enables the modification of numerous electroactive probes, thereby greatly improving the electrochemical signal. Under optimal conditions, a good linearity between the electrochemical signal and the logarithm of dsDNA-T concentration over the range from 1.0 fM to 1.0nM, with a detection limit of 0.47 fM, can be obtained. Results indicate that it is highly selective, and holds high anti-interference capability in the presence of human serum samples. Therefore, this method offers great promises in providing a universal and efficient solution for the direct detection of dsDNA.

Selectivity enhancements in gel-based DNA-nanoparticle assays by membrane-induced isotachophoresis: thermodynamics versus kinetics

Selectivity against mutant nontargets with a few mismatches remains challenging in nucleic acid sensing. Sensitivity enhancement by analyte concentration does not improve selectivity because it affects targets and nontargets equally. Hydrodynamic or electrical shear enhanced selectivity is often accompanied by substantial losses in target signals, thereby leading to poor limits of detection. We introduce a platform based on depletion isotachophoresis in agarose gel generated by an ion-selective membrane that allows both selectivity and sensitivity enhancement with a two-step assay involving concentration polarization at an ion-selective membrane. By concentrating both the targets and probe-functionalized nanoparticles by ion enrichment at the membrane, the effective thermodynamic dissociation constant is lowered from 40 nM to below 500 pM, and the detection limit is 10 pM as reported previously. A dynamically optimized ion depletion front is then generated from the membrane with a high electrical shear force to selectively and irreversibly dehybridize nontargets. The optimized selectivity against a two-mismatch nontarget (in a 35-base pairing sequence) is shown to be better than the thermodynamic equilibrium selectivity by more than a hundred-fold, such that there is no detectable signal from the two-mismatch nontarget. We offer empirical evidence that irreversible cooperative dehybridization plays an important role in this kinetic selectivity enhancement and that mismatch location controls the optimum selectivity even when there is little change in the corresponding thermodynamic dissociation constant.

Sequence specific recognition of HIV-1 dsDNA in the large amount of normal dsDNA based upon nicking enzyme signal amplification and triplex DNA

A sensitive fluorescent strategy for sequence specific recognition of HIV dsDNA was established based upon Nicking Enzyme Signal Amplification (NESA) and triplex formation. dsDNA sequence from the site 7960 to site 7991 of the HIV1 dsDNA gene was designed as target dsDNA, which was composed of two complementary strands Oligonucleotide 1 with the sequence of 3'-CTT CCT TAT CTT CTT CTT CCA CCT CTC TCT CT-5' (Oligo-1) and Oligonucleotide 2 with the sequence of 5'-GAA GGA ATA GAA GAA GAA GGT GGA GAG AGA GA-3' (Oligo-2). As a proof of concept, Oligonucleotide 5'-6-FAM-GAG GTG GAG CTG CGC GAC TCC TCC TCT CTC TCT CTC CAC CTC-BHQ-1-3'(Oligo-4) acted as molecular beacon(MB) probe, Oligonucleotide 5'-CTT CCT TAT CTT CTT CTT CCA AAA GGA GTC GCG-3' (Oligo-7) acted as assistant probe. In the presence of target dsDNA, Oligo-4 and Oligo-7 hybridized with target dsDNA through triplex formation and formed Y-shaped structure, NESA occurred with further addition of Nt.BbvCI, accompanied with the release of fluorescent DNA fragment circularly, resulted in the increase of fluorescence intensity. Under the optimum conditions, the fluorescence intensity was linear with the concentration of target dsDNA over the range from 100pM to 200nM, the linear regression equation was I = 1.266 C + 84.3 (C: nmol/L, R² = 0.991), with a detection limit of 65pM. Moreover, the effect of coexisted other dsDNA was investigated as well, and satisfactory results were obtained.

Efficient Fluorescence Resonance Energy Transfer between Quantum Dots and Gold Nanoparticles Based on Porous Silicon Photonic Crystal for DNA Detection

A novel assembled biosensor was prepared for detecting 16S rRNA, a small-size persistent specific for Actinobacteria. The mechanism of the porous silicon (PS) photonic crystal biosensor is based on the fluorescence resonance energy transfer (FRET) between quantum dots (QDs) and gold nanoparticles (AuNPs) through DNA hybridization, where QDs act as an emission donor and AuNPs serve as a fluorescence quencher. Results showed that the photoluminescence (PL) intensity of PS photonic crystal was drastically increased when the QDs-conjugated probe DNA was adhered to the PS layer by surface modification using a standard cross-link chemistry method. The PL intensity of QDs was decreased when the addition of AuNPs-conjugated complementary 16S rRNA was dropped onto QDs-conjugated PS. Based on the analysis of different target DNA concentration, it was found that the decrease of the PL intensity showed a good linear relationship with complementary DNA concentration in a range from 0.25 to 10 μM, and the detection limit was 328.7 nM. Such an optical FRET biosensor functions on PS-based photonic crystal for DNA detection that differs from the traditional FRET, which is used only in liquid. This method will benefit the development of a new optical FRET label-free biosensor on Si substrate and has great potential in biochips based on integrated optical devices.

A cyclometalated iridium(III) complex used as a conductor for the electrochemical sensing of IFN-γ

A novel iridium(III) complex was prepared and used as a conductor for sensitive and enzyme-free electrochemical detection of interferon gamma (IFN-γ). This assay is based on a dual signal amplification mechanism involving positively charged gold nanoparticles ((+)AuNPs) and hybridization chain reaction (HCR). To construct the sensor, nafion (Nf) and (+)AuNPs composite membrane was first immobilized onto the electrode surface. Subsequently, a loop-stem structured capture probe (CP) containing a special IFN-γ interact strand was modified onto the (+)AuNP surface via the formation of Au-S bonds. Upon addition of IFN-γ, the loop-stem structure of CP was opened, and the newly exposed "sticky" region of CP then hybridized with DNA hairpin-1 (H₁), which in turn opened its hairpin structure for hybridizing with DNA hairpin-2 (H₂). Happen of HCR between H₁ and H₂ thus generated a polymeric duplex DNA (dsDNA) chain. Meanwhile, the iridium(III) complex could interact with the grooves of the dsDNA polymer, producing a strong current signal that was proportional to IFN-γ concentration. Thus, sensitive detection of IFN-γ could be realized with a detection limit down to 16.3 fM. Moreover, satisfied results were achieved by using this method for the detection of IFN-γ in human serum samples.

A colorimetric sensing platform based upon recognizing hybridization chain reaction products with oligonucleotide modified gold nanoparticles through triplex formation

A novel colorimetric sensing strategy for biomolecule assay has been developed, which integrates the signal amplification of the hybridization chain reaction (HCR) with the assembly of gold nanoparticles (AuNPs) through triplex formation. In the presence of targets, the HCR process can be triggered, the HCR products are specifically recognized by triplex-forming oligonucleotide (TFO) functionalized AuNPs, accompanying the aggregation of AuNPs and a dramatic absorbance change at 522 nm. In addition, the DNA hairpin probes can form rigid triplex structures with TFO-functionalized AuNPs in the absence of targets, resulting in a negligible background signal. By taking advantage of this new biosensor platform, a broad range of targets, involving nucleic acids, small molecules and proteins, have been successfully determined with high sensitivity and selectivity, which may hold great potential for practical application.

An electricity-fluorescence double-checking biosensor based on graphene for detection of binding kinetics of DNA hybridization

In this paper, an electricity-fluorescence double-checking biosensor based on graphene materials has been presented for detection of DNA hybridization kinetics.

An aptasensor with dsDNA for rapid and highly sensitive detection of kanamycin in milk

Herein, we developed an aptasensor using double-stranded DNA (dsDNA) modified with cadmium sulfide (CdS) nanoparticles and gold nanoparticles (AuNPs) on a gold electrode (GE) for kanamycin detection.

Sensitive detection of miRNA by using hybridization chain reaction coupled with positively charged gold nanoparticles

Positively charged gold nanoparticles (+)AuNPs can adsorb onto the negatively charged surface of single-stranded DNA (ssDNA) or double-stranded DNA (dsDNA). Herein, long-range dsDNA polymers could form based on the hybridization chain reaction (HCR) of two hairpin probes (H₁ and H₂) by using miRNA-21 as an initiator. (+)AuNPs could adsorb onto the negatively charged surface of such long-range dsDNA polymers based on the electrostatic adsorption, which directly resulted in the precipitation of (+)AuNPs and the decrease of (+)AuNPs absorption spectra. Under optimal conditions, miRNA-21 detection could be realized in the range of 20 pM-10 nM with a detection limit of 6.8 pM. In addition, (+)AuNPs used here are much more stable than commonly used negatively charged gold nanoparticles ((−)AuNPs) in mixed solution that contained salt, protein or other metal ions. Importantly, the assay could realize the detection of miRNA in human serum samples.

Ultrasensitive electrochemical detection of miRNA-21 by using an iridium(III) complex as catalyst

The ultrasensitive electrochemical detection of miRNA-21 was realized by using a novel redox and catalytic "all-in-one" mechanism with an iridium(III) complex as a catalyst. To construct such a sensor, a capture probe (CP) was firstly immobilized onto the gold electrode surface. In the presence of miRNA-21, a sandwiched DNA complex could form between CP and a methylene blue (MB) labeled G-rich detection probe modified onto a gold nanoparticle (AuNP) surface (DP-AuNPs). Upon addition of K(+), the structure of DP changed to a G-quadruplex. Then, the iridium(III) complex could selectively interact with the G-quadruplex, catalyzing the reduction of H2O2, which was accompanied by an electrochemical signal change using MB as an electron mediator. Under optimal conditions, the electrochemical signal of MB reduction peak was proportional to miRNA concentration in the range from 5.0 fM to 1.0 pM, with a detection limit of 1.6 fM. In addition, satisfactory results were obtained for miRNA-21 detection in human serum samples, indicating a potential application of the sensor for bioanalysis.

Sensitive detection of multiple pathogens using a single DNA probe

A simple but promising electrochemical DNA nanosensor was designed, constructed and applied to differentiate a few food-borne pathogens. The DNA probe was initially designed to have a complementary region in Vibrio parahaemolyticus (VP) genome and to make different hybridization patterns with other selected pathogens. The sensor was based on a screen printed carbon electrode (SPCE) modified with polylactide-stabilized gold nanoparticles (PLA-AuNPs) and methylene blue (MB) was employed as the redox indicator binding better to single-stranded DNA. The immobilization and hybridization events were assessed using differential pulse voltammetry (DPV). The fabricated biosensor was able to specifically distinguish complementary, non-complementary and mismatched oligonucleotides. DNA was measured in the range of 2.0×10(-9)-2.0×10(-13)M with a detection limit of 5.3×10(-12)M. The relative standard deviation for 6 replications of DPV measurement of 0.2µM complementary DNA was 4.88%. The fabricated DNA biosensor was considered stable and portable as indicated by a recovery of more than 80% after a storage period of 6 months at 4-45°C. Cross-reactivity studies against various food-borne pathogens showed a reliably sensitive detection of VP.

Application of iridium(III) complex in label-free and non-enzymatic electrochemical detection of hydrogen peroxide based on a novel "on-off-on" switch platform

We herein report a label-free and non-enzymatic electrochemical sensor for the highly sensitive detection of hydrogen peroxide (H2O2) based on a novel "on-off-on" switch system. In our design, MB was used as an electron mediator to accelerate the electron transfer while AuNPs was used to amplify the electrochemical signal due to its excellent biocompatibility and good conductivity. The "switch-off" state was achieved by introducing the guanine-rich capture probe (CP) and an iridium complex onto the electrode surface to form a hydrophobic layer, which then hinders electron transfer. Upon addition of H2O2, fenton reaction occurs and produces OH• in the presence of Fe(2+). The OH• cleaves the CP into DNA fragments, thus resulting in the release of CP and iridium complex from the sensing interface, recovering the electrochemical signal to generate a "switch-on" state. Based on this novel switch system, a detection limit as low as 3.2 pM can be achieved for H2O2 detection. Moreover, satisfactory results were obtained by using this method for the detection of H2O2 in sterilized milk. To the best of our knowledge, this is the first G-quadruplex-based electrochemical sensor using an iridium(III) complex.

Ultrasensitive electrochemical detection of protein tyrosine kinase-7 by gold nanoparticles and methylene blue assisted signal amplification

We present here an ultrasensitive and simple strategy for protein tyrosine kinase-7 (PTK7) detection based on the recognition-induced structure change of sgc8 aptamer, and the signal change of methylene blue (MB) that interacted with sandwiched DNA complex. To construct such a sensor, an homogeneous nano-surface was formed firstly on the glass carbon electrode (GCE) by using negatively charged Nafion (Nf) as the inner layer and positively charged gold nanoparticles ((+)AuNPs) as the outer layer, followed by the immobilization of sgc8 aptamer based on Au-S bond. In the presence of helper probe (HP), sandwiched DNA complex was formed between the sgc8 aptamer and the DNA modified gold nanoparticle probe (DNA-AuNPs). Then, a strong current signal was produced due to the capture of abundant MB molecules by both the sandwiched DNA complex and the multiple DNAs that modified on AuNPs surface. However, the specific binding of sgc8 aptamer with PNK7 would trigger a structure transition of it, and directly prevented the following formation of sandwiched structure and the capture of MB. Thus, PTK7 detection could be realized based on monitoring the signal reduction of MB upon incubation of sgc8 aptamer with PTK7. Under optimal conditions, a low detection limit of 372 fM was obtained for PNK7 detection. Due to the employment of sgc8 aptamer, the proposed biosensor exhibited high selectivity to PNK7. Moreover, satisfactory results were obtained when the proposed method was applied for PNK7 detection in cellular debris.

Fluorescence recognition of double-stranded DNA based on the quenching of gold nanoparticles to a fluorophore labeled DNA probe

This work described an ultrasensitive fluorescent sensor for sequence-specific recognition of dsDNA based on the quenching of gold nanoparticles (AuNPs) to a fluorophore labeled DNA probe.