DNA molecular beacon-based plastic biochip: a versatile and sensitive scanometric detection platform

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.

Paving the way towards continuous biosensing by implementing affinity-based nanoswitches on state-dependent readout platforms

Combining affinity-based nanoswitches with state-dependent readout platforms allows for continuous biosensing and acquisition of real-time information about biochemical processes occurring in the environment of interest.

High-Throughput Single-Cell Extracellular Vesicle Secretion Analysis on a Desktop Scanner without Cell Counting

Single-cell EV (extracellular vesicle) secretion analysis is emerging for a better understanding of non-genetic cellular heterogeneity regulating human health and diseases through intercellular mediators. However, the requirements of expensive and bulky instrumentations hinder its widespread use. Herein, by combining gold nanoparticle-enhanced silver staining and the Poisson distribution, we reported the use of a home-use scanner to realize high-throughput single-cell EV secretion analysis without cell counting. We applied the platform to analyze the secretions of different EV phenotypes with the human oral squamous cell carcinoma cell line and primary cells from patients, which generated single-cell results comparable with those of the immunofluorescence approach. Notably, we also realized the quantification of the number of EVs secreted from every single cell using their respective titration curves obtained from population samples, making it possible to directly compare different EV phonotypes in regard to their secretion number, secretion rate, and so forth. The technology introduced here is simple, easy to operate, and of low cost, which make it a potential, easily accessible, and affordable tool for widespread use in both basic and clinical research.

Detection of Mercury Ion with High Sensitivity and Selectivity Using a DNA/Graphene Oxide Hybrid Immobilized on Glass Slides

Excessive mercury ions (Hg²⁺) cause great pollution to soil/water and pose a major threat to human health. The high sensitivity and high selectivity in the Hg²⁺ detection demonstrated herein are significant for the research areas of analytical chemistry, chemical biology, physical chemistry, drug discovery, and clinical diagnosis. In this study, a series of simple, low-cost, and highly sensitive biochips based on a graphene oxide (GO)/DNA hybrid was developed. Hg²⁺ is detected with high sensitivity and selectivity by GO/DNA hybrid biochips immobilized on glass slides. The performance of the biosensors can be improved by introducing more phosphorothioate sites and complementary bases. The best limit of detection of the biochips is 0.38 nM with selectivity of over 10:1. This sensor was also used for Hg²⁺ detection in Dendrobium. The results show this biochip is promising for Hg²⁺ detection.

A versatile fluorometric in situ hybridization method for the quantitation of hairpin conformations in DNA self-assembled monolayers

As the performance of hairpin DNA (hpDNA)-based biosensors is highly dependent on the yield of stem-loop (hairpin) conformations, we report herein a versatile fluorometric in situ hybridization protocol for examining hpDNA self-assembled monolayers (SAMs) on popularly used biochip substrates. Specifically, the ratio of fluorescence (FL) intensities of hpDNA SAMs (in an array format) before and after hybridization was adopted as the key parameter for performing such a determination. Upon confirming the existence of mixed and tunable DNA conformations in binary deposition solutions and efficient hybridization of the hairpin strands with the target DNA via gel electrophoresis assays, we tested the fluorometric protocol for determining the coverages of hpDNA in hpDNA/ssDNA SAMs prepared on gold; its accuracy was validated by Exonuclease I (Exo I)-assisted electrochemical quantitation. To further confirm its versatility, this FL protocol was adopted for quantifying hairpin conformations formed on glass and polycarbonate (PC) substrates. The molar ratios of surface-tethered hairpin conformations on the three different substrates were all found to be proportional to but less than those in the binary deposition solutions, and were dependent on the substrate morphology. The findings reported herein are beneficial for the construction of highly efficient DNA hairpin-based sensing surfaces, which essentially facilitates the creation of hpDNA-based biosensors with optimal detection performance.

Amperometric Aptasensor for Amyloid-β Oligomer Detection by Optimized Stem-Loop Structures with an Adjustable Detection Range

Amyloid-β oligomers (AβO) have become representative biomarkers for early diagnosis of Alzheimer's disease. Here, we report on an aptasensor based on stem-loop probes for sensitive and specific detection of AβO by an amperometric transducer principle using alternating current voltammetry (ACV). Stem-loop probes with redox-active moieties are immobilized on a gold substrate as a receptor element. The signal transduction mechanism relies on redox ferrocene (Fc) reporting via charge transfer on a molecular recognition event involving a conformational change of the molecular beacon. The stem-loop structures were optimized by considering the aptamers' stem length, spacer, and different ferrocene terminals. In addition, the sensor assembly and signal recording including aptamer concentration and ACV frequency dependence are discussed. Using the optimized stem-loop probe (B-3' Fc), the aptasensor showed a decrease of the Fc peak current induced by AβO binding within the broad concentration range spanning 6 orders of magnitude. Furthermore, the detection limit of the sensor can be further decreased by optimizing the ACV frequency, however at the cost of a narrowed detection range. In this work, a label-free electrochemical aptasensor is demonstrated, which facilitates the quantification of the concentration of AβO with high selectivity and subpicomolar sensitivity, which may be conducive to improving the diagnosis and pharmacology studies of Alzheimer's disease.

Blu-Ray Discs as Universal Biochip Substrates: Lithography-Free Surface Activation and Assay Patterning

Blu-ray discs (BDs) are advantageous in comparison with other optical discs (compact discs and digital versatile discs) in terms of not only their storage capacity but also the high-quality materials fabricated from. We have recently discovered that the "Hard Coat" film of Verbatim BDs is in fact a unique type of polymeric substrates that can be readily activated and adapted for biochip fabrications. Particularly, the Hard Coat film peeled from BDs is optically transparent without any fluorescence background, which can be activated by treating with a common base (1.0 M NaOH) at a slightly elevated temperature (55 °C). The surface density of reactive carboxylic acid groups generated, 6.6 ± 0.7 × 10^-9 mol/cm², is much higher than that on polycarbonate upon UV/ozone irradiation (4.8 ± 0.2 × 10^-10 mol/cm²). There are no significant physical damages to the substrate morphology, and the aging effect is minimal. More importantly, the BD substrate can be patterned using either cut-out filter paper masks or microfluidic channel plates; both are lithography-free, bench-top methods that facilitate the device fabrication in a common laboratory setting. With classical biotin-streptavidin binding and DNA hybridization arrays as trial systems, we have also demonstrated this new type of biochip substrates for quantitative assay applications.

Duplexed aptamers: history, design, theory, and application to biosensing

Nucleic acid aptamers are single stranded DNA or RNA sequences that specifically bind a cognate ligand. In addition to their widespread use as stand-alone affinity binding reagents in analytical chemistry, aptamers have been engineered into a variety of ligand-specific biosensors, termed aptasensors. One of the most common aptasensor formats is the duplexed aptamer (DA). As defined herein, DAs are aptasensors containing two nucleic acid elements coupled via Watson-Crick base pairing: (i) an aptamer sequence, which serves as a ligand-specific receptor, and (ii) an aptamer-complementary element (ACE), such as a short DNA oligonucleotide, which is designed to hybridize to the aptamer. The ACE competes with ligand binding, such that DAs generate a signal upon ligand-dependent ACE-aptamer dehybridization. DAs possess intrinsic advantages over other aptasensor designs. For example, DA biosensing designs generalize across DNA and RNA aptamers, DAs are compatible with many readout methods, and DAs are inherently tunable on the basis of nucleic acid hybridization. However, despite their utility and popularity, DAs have not been well defined in the literature, leading to confusion over the differences between DAs and other aptasensor formats. In this review, we introduce a framework for DAs based on ACEs, and use this framework to distinguish DAs from other aptasensor formats and to categorize cis- and trans-DA designs. We then explore the ligand binding dynamics and chemical properties that underpin DA systems, which fall under conformational selection and induced fit models, and which mirror classical SN1 and SN2 models of nucleophilic substitution reactions. We further review a variety of in vitro and in vivo applications of DAs in the chemical and biological sciences, including riboswitches and riboregulators. Finally, we present future directions of DAs as ligand-responsive nucleic acids. Owing to their tractability, versatility and ease of engineering, DA biosensors bear a great potential for the development of new applications and technologies in fields ranging from analytical chemistry and mechanistic modeling to medicine and synthetic biology.

Single-stranded DNA modified protonated graphitic carbon nitride nanosheets: A versatile ratiometric fluorescence platform for multiplex detection of various targets

Facile and cost-effective detection of multiple targets is essential for a variety of applications ranging from life sciences to environmental monitoring. Here, we report a versatile ratiometric fluorescence platform for multiple detection of various targets based on the conjugation of single-stranded DNA (ssDNA) with protonated graphitic carbon nitride nanosheets (Pg-C₃N₄ NSs). We demonstrate that intrinsic peroxidase-like activity of Pg-C₃N₄ NSs is enhanced by conjugating with ssDNA, and thus the oxidation of substrate o-phenylenediamine (OPD) is promoted in the presence of H₂O₂. The oxidation product 2,3-diaminophenazine (DAP) can deliver a new fluorescence signal at 564 nm, and concurrently quench the intrinsic fluorescence of conjugates ssDNA/Pg-C₃N₄ NSs at 443 nm upon excitation at 370 nm. The transformation of fluorescence provides us a novel strategy for ratiometric fluorescence-based analytical sensing. Taking ssDNA as the target-recognition element of the conjugates ssDNA/Pg-C₃N₄ NSs, we favorably present ratiometric fluorescence detection of various targets including heavy metal ions (Hg²⁺) and biomolecules (Aflatoxin B1 (AFB1) and adenosine triphosphate (ATP)) in real samples by varying the ssDNA sequences. The present work provides a new strategy to develop facile methods for quantitative determination of various analytes and uncovers an innovative horizon for Pg-C₃N₄ NSs-based sensing platform fabrication.

Simple and Sensitive Quantification of MicroRNAs via PS@Au Microspheres-Based DNA Probes and DSN-Assisted Signal Amplification Platform

Identifying the microRNA (miRNA) expression level can provide critical information for early diagnosis of cancers or monitoring the cancer therapeutic efficacy. This paper focused on a kind of gold-nanoparticle-coated polystyrene microbeads (PS@Au microspheres)-based DNA probe as miRNA capture and duplex-specific nuclease (DSN) signal amplification platform based on an RGB value readout for detection of miRNAs. In virtue of the outstanding selectivity and simple experimental operation, 5'-fluorochrome-labeled molecular beacons (MBs) were immobilized on PS@Au microspheres via their 3'-thiol, in the wake of the fluorescence quenching by nanoparticle surface energy transfer (NSET). Target miRNAs were captured by the PS@Au microspheres-based DNA probe through DNA/RNA hybridization. DSN enzyme subsequently selectively cleaved the DNA to recycle the target miRNA and release of fluorophores, thereby triggering the signal amplification with more free fluorophores. The RGB value measurement enabled a detection limit of 50 fM, almost 4 orders of magnitude lower than PS@Au microspheres-based DNA probe detection without DSN. Meanwhile, by different encoding of dyes, miRNA-21 and miRNA-10b were simultaneously detected in the same sample. Considering the ability for quantitation, high sensitivity, and convenient merits, the PS@Au microspheres-based DNA probe and DSN signal amplification platform supplied valuable information for early diagnosis of cancers.

Scanometry as microplate reader for high throughput method based on DPPH dry reagent for antioxidant assay

The stable chromogenic radical 1,1'-diphenyl-2-picrylhydrazyl (DPPH) solution was immobilized on the microwell plate as dry reagent to construct a simple antioxidant sensor. Then, a regular flatbed scanner was used as microplate reader to obtain analytical parameters for antioxidant assay using one-shot optical sensors as scanometry technique. Variables affecting the acquisition of the images were optimized and the analytical parameters are obtained from an area of the sensing zone inside microwell using the average luminosity of the sensing zone captured as the mean of red, green, and blue (RGB) value using ImageJ^® program. By using this RGB value as sensor response, it is possible to determine antioxidant capacity in the range 1-25 ppm as gallic acid equivalent (GAE) with the response time of 9 min. The reproducibility of sensor was good (RSD<1%) with recovery at 93%-96%. The antioxidant sensor was applied to the plant extracts, such as sappan wood and Turmeric Rhizome. The results are good when compared to the same procedure using a UV/Vis spectrophotometer.

Selective staining of CdS on ZnO biolabel for ultrasensitive sandwich-type amperometric immunoassay of human heart-type fatty-acid-binding protein and immunoglobulin G

We report on an ultrasensitive metal-labeled amperometric immunoassay of proteins, which is based on the selective staining of nanocrystalline cadmium sulfide (CdS) on ZnO nanocrystals and in-situ microliter-droplet anodic stripping voltammetry (ASV) detection on the immunoelectrode. Briefly, antibody 1 (Ab₁), bovine serum albumin (BSA), antigen and ZnO-multiwalled carbon nanotubes (MWCNTs) labeled antibody 2 (Ab₂-ZnO-MWCNTs) were successively anchored on a β-cyclodextrin-graphene sheets (CD-GS) nanocomposite modified glassy carbon electrode (GCE), forming a sandwich-type immunoelectrode (Ab₂-ZnO-MWCNTs/antigen/BSA/Ab₁/CD-GS/GCE). CdS was selectively grown on the catalytic ZnO surfaces through chemical reaction of Cd(NO₃)₂ and thioacetamide (ZnO-label/CdS-staining), due to the presence of an activated cadmium hydroxide complex on ZnO surfaces that can decompose thioacetamide. A beforehand cathodic "potential control" in air and then injection of 7μL of 0.1M aqueous HNO₃ on the immunoelectrode allow dissolution of the stained CdS and simultaneous cathodic preconcentration of atomic Cd onto the electrode surface, thus the following in-situ ASV detection can be used for immunoassay with enhanced sensitivity. Under optimized conditions, human immunoglobulin G (IgG) and human heart-type fatty-acid-binding protein (FABP) are analyzed by this method with ultrahigh sensitivity, excellent selectivity and small reagent-consumption, and the limits of detection (LODs, S/N=3) are 0.4fgmL^-1 for IgG and 0.3fgmL^-1 for FABP (equivalent to 73 FABP molecules in the 6μL sample employed).

An antifouling electrochemical immunosensor for carcinoembryonic antigen based on hyaluronic acid doped conducting polymer PEDOT

A sensitive and antifouling electrochemical CEA immunosensor was developed based on PEDOT doped with hyaluronic acid.

Binary DNA hairpin-based colorimetric biochip for simultaneous detection of Pb2+ and Hg2+ in real-world samples

A novel microarray-format colorimetric biochip was constructed for simultaneously detecting the trace amounts of Pb²⁺ and Hg²⁺ in various real-world samples.

Toward point-of-care diagnostics with consumer electronic devices: the expanding role of nanoparticles

A review of the role that nanoparticles can play in point-of-care diagnostics that utilize consumer electronic devices such as cell phones and smartphones for readout, including an overview of important concepts and examples from the literature.