On-chip aptamer-based sandwich assay for thrombin detection employing magnetic beads and quantum dots

Recent Advances in Biomolecular Detection Based on Aptamers and Nanoparticles

The fast, accurate detection of biomolecules, ranging from nucleic acids and small molecules to proteins and cellular secretions, plays an essential role in various biomedical applications. These include disease diagnostics and prognostics, environmental monitoring, public health, and food safety. Aptamer recognition (DNA or RNA) has gained extensive attention for biomolecular detection due to its high selectivity, affinity, reproducibility, and robustness. Concurrently, biosensing with nanoparticles has been widely used for its high carrier capacity, stability and feasibility of incorporating optical and catalytic activity, and enhanced diffusivity. Biosensors based on aptamers and nanoparticles utilize the combination of their advantages and have become a promising technology for detecting of a wide variety of biomolecules with high sensitivity, reliability, specificity, and detection speed. Via various sensing mechanisms, target biomolecules have been quantified in terms of optical (e.g., colorimetric and fluorometric), magnetic, and electrical signals. In this review, we summarize the recent advances in and compare different aptamer-nanoparticle-based biosensors by nanoparticle types and detection mechanisms. We also share our views on the highlights and challenges of the different nanoparticle-aptamer-based biosensors.

A facile aptamer-based sensing strategy for dopamine detection through the fluorescence energy transfer between dye and single-wall carbon nanohorns

Dopamine (DBA) as an important biomarker, plays a crucial role in disease diagnosis. In this study, we have developed a fast and simple aptamer-based fluorescence strategy which used single-wall carbon nanohorns (SWCNHs) as a quencher for dopamine detection. SWCNHs were negatively charged after pretreated, which improved its dispersion in solution. 5-carboxy-fluorescein (FAM) was used to label dopamine aptamer. In the absence of dopamine, FAM-modified aptamer could be absorbed onto the SWCNHs surface due to π-π interaction, resulting in the fluorescence intensity decreased. Dopamine could specifically bind with FAM-DNA to form G-quadruplex, which could not be absorbed onto the surface of SWCNHs. Hence, the fluorescence of FAM-DNA recovered, and the fluorescent intensity as a function of different concentrations of dopamine was measured. We obtained a detection limit of 5 μM for this detection system with a linear detection range of 0.02-2.20 mM. Furthermore, the feasibility of the innovative detection system has been verified by detecting dopamine in spiked serum samples.

Detection of Alpha-Fetoprotein Using Aptamer-Based Sensors

Alpha-fetoprotein (AFP) is widely-known as the most commonly used protein biomarker for liver cancer diagnosis at the early stage. Therefore, developing the highly sensitive and reliable method of AFP detection is of essential demand for practical applications. Herein, two types of aptamer-based AFP detection methods, i.e., optical and electrochemical biosensors, are reviewed in detail. The optical biosensors include Raman spectroscopy, dual-polarization interferometry, resonance light-scattering, fluorescence, and chemiluminescence. The electrochemical biosensors include cyclic voltammetry, electrochemical impedance spectroscopy, and giant magnetic impedance. Looking into the future, methods for AFP detection that are high sensitivity, long-term stability, low cost, and operation convenience will continue to be developed.

Dual-aptamer-based enzyme linked plasmonic assay for pathogenic bacteria detection

Development of rapid, sensitive, and selective method for pathogenic bacteria detection is of great importance for food safety, medical diagnostic, and environmental monitoring. Currently, most techniques for low numbers of bacteria detection require advanced instrumentation or skilled operators. Herein, we present a facile colorimetric detection platform for bacterial detection using Ag nanoplates as chromogenic substrate, which takes advantages of the high specificity and affinity of aptamer and the ability of catalase to hydrolyze H₂O₂ that can etch Ag nanoplates. By introducing catalase to the sandwich structure composed by dual-aptamer recognition strategy, bacteria detection signal is converted to the peak shift of LSPR and colorimetric change. This proposed method allows a fast naked-eye detection of S. aureus at the concentration of 60 CFU/mL based on the combination of streptavidin-biotin system and inherent sensitivity of plasmonic Ag nanoplates. Owing to the high selectivity and sensitivity, as well as the low-cost and good adaptability, this plasmonic assay is expected to be suitable for pathogenic bacteria detection in resource-limited settings.

Bio-nanocapsules for oriented immobilization of DNA aptamers on aptasensors

The oriented immobilization of sensing molecules (e.g., IgGs, receptors, lectins, and DNA aptamers) on sensor chips is particularly important for maximizing the potential of the sensing molecules, thereby enhancing the sensitivity and target-binding capacity of biosensors. We previously developed ∼30 nm bio-nanocapsules (ZZ-BNCs) consisting of the hepatitis B virus envelope L protein fused with the tandem form of protein A-derived IgG Fc-binding Z domain (ZZ-L protein). ZZ-BNC acts successfully as a scaffold, enhancing both the sensitivity and binding capacity of IgG, a Fc-fused receptor, and Fc-fused lectin to antigens, cytokines, and sugar chains through an oriented immobilization on a biosensor surface. To expand the versatility of ZZ-BNC, we modified ZZ-BNC by replacing the ZZ domain with a DNA-binding single-chain lambda Cro (scCro) domain, thereby developing scCro-BNC. The scCro-BNC was synthesized in yeast cells and homogeneously purified as ∼30 nm sized nanoparticles. In a quartz crystal microbalance, an scCro-BNC-coated sensor chip immobilized with thrombin-binding DNA aptamers showed an ∼5.5-fold higher thrombin-binding capacity and ∼6000-fold higher detection sensitivity than a sensor chip directly coated with DNA aptamers. In addition, the number of bound thrombin molecules per molecule of DNA aptamer increased by ∼7.8-fold with an scCro-BNC coating, consistent with the theoretical thrombin-binding capacity. Collectively, scCro-BNC was shown to perform as an ideal scaffold for maximizing the potential of the DNA aptamer by immobilizing it in an oriented manner. Facilitating a highly sensitive detection of various target molecules, these BNC-based scaffolds are expected to improve a wide range of biosensors while minimizing the number of sensing molecules required.

Transcription-Based Amplified Colorimetric Thrombin Sensor Using Non-Crosslinking Aggregation of DNA-Modified Gold Nanoparticles

Gold nanoparticles (AuNPs) have been employed as colorimetric biosensors due to the color difference between their dispersed (red) and aggregated (blue) states. Although signal amplification reactions triggered by structural changes of the ligands on AuNPs have been widely used to improve measurement sensitivity, the use of ligands is limited. In this study, we designed a AuNP-based signal-amplifying sandwich biosensor, which does not require a conformational change in the ligands. Thrombin was used as a model target, which is recognized by two different probes. In the presence of the target, an extension reaction occurs as a result of hybridization of the two probes. Then RNA synthesis is started by RNA polymerase activation due to RNA promoter duplex formation. The amplified RNA drives aggregation or dispersion of the AuNPs, and a difference of the color if the AuNP solution is observed. As this detection system does not require a conformational change in the ligand, it can be generically applied to a wide range ligands.

Microfluidic Magnetic Analyte Delivery Technique for Separation, Enrichment, and Fluorescence Detection of Ultratrace Biomarkers

A microfluidic magnetic analyte delivery (μMAD) technique was developed to realize sample preparation and ultrasensitive biomarker detection. A simply designed microfluidic device was employed to carry out this technique, including a poly(dimethylsiloxane)-glass hybrid microchip having four straight rectangular channels and a permanent magnet. In the μMAD process, functionalized magnetic beads (MBs) were used to recognize and isolate analytes from a complex sample matrix, deliver analytes into tiny microchannels, and preconcentrate analytes in the magnetic trapping/detection region for in situ fluorescence detection. In the feasibility study and sensitivity optimization, horseradish peroxidase-labeled MBs were used, and critical parameters for the signal amplification performance of μMAD were carefully evaluated. At optimized conditions, a sensitivity improvement of at least 2 orders of magnitude was achieved. As a proof of concept, μMAD was combined with the enzyme-linked immunosorbent assay (ELISA), while carcinoembryonic antigen (CEA), prostate-specific antigen (PSA), and interleukin 6 (IL-6) were selected as model biomarkers. The limits of detection (LODs) of μMAD-ELISA were as low as 0.29 pg/mL for CEA, 0.047 pg/mL for PSA, and 0.021 pg/mL for IL-6, which corresponded to an over 200-fold reduction compared to their commercial ELISA results. Meanwhile, μMAD-ELISA revealed high selectivity and reproducibility. In clinical sample analysis, good accuracy was acquired for human serum analysis relative to commercial ELISA kits, and satisfied recoveries of 85.1-102% with RSDs of 1.7-9.8% for IL-6 and 84.7-113% with RSDs of 3.2-8.3% for interferon-γ were obtained. This ultrasensitive and easy operation technique provides a valuable approach for trace-level biomarker detection for practical applications.

Convenient Construction of Orthogonal Dual Aptamer-Based Plasmonic Immunosandwich Assay for Probing Protein Disease Markers in Complex Samples and Living Animals

Aptamers, because of their outstanding merits including simple synthesis and easy modification, have been widely used as antibody alternatives to construct novel immunosandwich assays. Dual aptamer-based sandwich assays exhibit multiple advantages over conventional immunosandwich assays and single aptamer-based sandwich assays. However, their construction is hampered by the limited knowledge of binding orthogonality of aptamers reported in the literature. Herein, we present a new strategy for conveniently constructing an orthogonal dual aptamer-based plasmonic immunosandwich assay (odA-PISA) for probing proteins in complex samples and living animals. An orthogonal aptamer pair was first efficiently selected from the aptamers reported in the literature by affinity capillary electrophoresis. Then, a target protein-capturing gold thin-layer-coated probe and silver nanoparticle-based Raman labeling nanotags were conveniently prepared with the selected aptamers and used to construct the assay. The double aptamers used ensured the specificity, whereas the plasmonic coupling effect between the target-capturing probe and the generated Raman nanotags significantly enhanced the Raman signal intensity, providing high sensitivity. As a proof of principle, alkaline phosphatase (ALP) was used as the target. The constructed odA-PISA exhibited high specificity and high sensitivity toward ALP, giving cross-reactivity ≤ 4.2% and the limit of detection of 3.8 pM (S/N = 4). The quantitative determination of ALP in human serum and probing ALP in tumor-bearing mice were achieved, showing the great application potential of the method. This strategy is widely applicable to other protein disease markers. Therefore, it opened a new access to the construction of sensitive dual aptamer-based sandwich assays for real-world applications, particularly disease diagnosis.

Advances in aptasensor technology

Aptasensors form a class of biosensors that function on the basis of a biological recognition. An aptasensor is advantageous because it incorporates a unique biologic recognition element, i.e., an aptamer, coupled to a transducer to convert a biological interaction to readable signals that can be easily processed and reported. In such biosensors, the specificity of aptamers is comparable to and sometimes even better than that of antibodies. Using the SELEX technique, aptamers with high specificity and affinity to various targets can be isolated from large pools of different oligonucleotides. Nowadays, new modifications of the SELEX technique and, as a result, easy generation and synthesis of aptamers have led to the wide application of these materials as biological receptors in biosensors. In this regard, aptamers promise a bright future. In the present research a brief account is initially provided of the recent developments in aptasensors for various targets. Then, immobilization methods, design strategies, current limitations and future directions are discussed for aptasensors.

Microfluidics in Haemostasis: A Review

Haemostatic disorders are both complex and costly in relation to both their treatment and subsequent management. As leading causes of mortality worldwide, there is an ever-increasing drive to improve the diagnosis and prevention of haemostatic disorders. The field of microfluidic and Lab on a Chip (LOC) technologies is rapidly advancing and the important role of miniaturised diagnostics is becoming more evident in the healthcare system, with particular importance in near patient testing (NPT) and point of care (POC) settings. Microfluidic technologies present innovative solutions to diagnostic and clinical challenges which have the knock-on effect of improving health care and quality of life. In this review, both advanced microfluidic devices (R&D) and commercially available devices for the diagnosis and monitoring of haemostasis-related disorders and antithrombotic therapies, respectively, are discussed. Innovative design specifications, fabrication techniques, and modes of detection in addition to the materials used in developing micro-channels are reviewed in the context of application to the field of haemostasis.

Micro-nanoparticles magnetic trap: Toward high sensitivity and rapid microfluidic continuous flow enzyme immunoassay

In this work, we developed a microfluidic system for immunoassays where we combined the use of magnetic nanoparticles as immunosupport, a microfluidic magnetic trap, and a fluorogenic substrate in continuous flow for detection which, together with the optimization of the functionalization of surfaces to minimize nonspecific interactions, resulted in a detection limit in the order of femtomolar and a total assay time of 40 min for antibiotin antibody detection. A magnetic trap made of carbonyl-iron microparticles packaged inside a 200  μ m square microchannel was used to immobilize and concentrate nanoparticles. We functionalized the surface of the iron microparticles with a silica-polyethylene glycol (PEG) shell to avoid corrosion and unspecific protein binding. A new one-step method was developed to coat acrylic microchannels with an organofunctional silane functionalized with PEG to minimize unspecific binding. A model immunoassay was performed using nanoparticles decorated with biotin to capture antibiotin rabbit Immunoglobulin G (IgG) as target primary antibody. The detection was made using antirabbit IgG labeled with the enzyme alkaline phosphatase as a secondary antibody, and we measured fluorescence with a fluorescence microscope. All steps of the immunoassay were performed inside the chip. A calibration curve was obtained in which a detection limit of 8 pg/ml of antibiotin antibody was quantified. The simplicity of the device and the fact that it is made of acrylic, which is compatible with mass production, make it ideal for Point-Of-Care applications.

Selective, sensitive, and fast determination of S-layer proteins by a molecularly imprinted photonic polymer coated film and a fiber-optic spectrometer

A newly developed molecularly imprinted photonic polymer (MIPP) film, which was prepared by colloidal crystal templating and surface molecular imprinting, was used for selective capture of S-layer protein (SLP) from a complex Lactobacillus acidophilus sample. The colloidal crystal templates were formed by a dipping process followed by chemical binding of the imprinted template SLP molecules. A sandwich structure consisting of two glass slides was formed after the SLP-silica layer had been covered with a poly(methyl methacrylate) glass slide. After polymerization of the SLP-silica layer with the preprepared polymerization solution, hydrofluoric acid and acetic phosphate buffer solutions removed the silica particles and SLP molecules, respectively. The MIPP film obtained exhibited a three-dimensional, highly ordered and interconnected macroporous structure (pore size greater than 200 nm), which is specifically accessible to SLP molecules. The adsorbed SLP molecules were simply and straightforwardly detected by a fiber-optic spectrometer. The redshift of the Bragg diffraction peak of the MIPP film was linearly related to the number of SLP molecules that had been harvested in the film. The detection limit of the SLP-MMIP-fiber-optic spectrometer method for SLP was 1 ng mL^-1. The MIPP sensor was successfully applied to detect SLP molecules in a crudely extracted Lactobacillus acidophilus sample. Our results prove the applicability of the SLP-MIPP film for fast and real-time measurement of SLP. Graphical abstract.

Enhancement of Eu3+ Emission in YVO4:Eu3+ Nanocrystals by Li+ Codoping: An Oxidant-Resistant Dispersion and Polymer Film

The enhancement of red emission of YVO₄:Eu³⁺ nanocrystals by Li⁺ codoping has been achieved. The effect of Li⁺ codoping on the crystalline properties and the luminescence of Eu³⁺ has been thoroughly studied. An increase of the unit cell volume and crystallinity of the nanocrystals is observed as the concentration of Li⁺ codoping increases. The lattice expansion could be related to occupation of the interstitial sites by the Li⁺ ions. The nanocrystals appear to be assemblies of rodlike nanostructures along with cube-shaped rough nanostructures of uniform size. The optimum concentration of Li⁺ codoping for luminescence enhancement is found to be 5 at. % at which Eu³⁺ emission is increased by about 2.5 times. The fall in Eu³⁺ emission after codoping of Li⁺ (7-15 at. %) is observed. Is it the increased crystallinity (i.e., the size) or the lattice expansion that poses a limit to luminescence enhancement? Annealing at 500 and 850 °C increased the luminescence emission by threefold and fivefold, respectively. The samples are readily dispersible in deionized water and incorporated easily in the flexible polymer film made of polyvinylidene fluoride. The dispersion-in-water shows bright red luminescence as low as 50 μg/mL. The emission intensity of the dispersion decreases linearly with concentration with a slope almost equal to unity. The dispersion and the flexible film do not show luminescence degradation under the influence of oxidizing H₂O₂ medium. The oxidant-resistant nature with enhanced luminescence could serve as a suitable red emitter for lighting and display applications.

The behavior of a bipedal DNA walker moving on the surface of magnet microparticles and its application in DNA detection

In this work, a three-dimensional DNA machine based on the isothermal strand-displacement polymerase reaction (ISDPR) has been constructed. The walking behavior of a DNA walker on the obstructive surface of magnetic beads has also been studied by adding different nucleic acid blocks. The "leg" of the DNA walker could hybridize with a hairpin structure DNA named H1 and lead to the opening of it. And the newly exposed stem would interact with a primer. A strand exchange has happened with the assistance of polymerase and dNTPs, so that the "leg" has been displaced and the DNA walker could be pushed to move on the surface. But the nucleic acid blocks could increase steric hindrance and obstruct this process, which is similar to the behavior of human beings walking on craggy paths. Through changing these blocks, such as the structure, the amount, and the length of blocks, the movement of the DNA walker has been controlled. What's more, the results of its application for DNA detection are satisfactory. The limit of detection is 21.6 pM. Also, this method has been successfully applied in complex biological samples. Graphical abstract ᅟ.

Biomass-based quantum dots co-doped with sulfur and nitrogen for highly sensitive detection of thrombin and its inhibitor

A biomass-based quantum dots co-doped with sulfur and nitrogen was prepared by using garlic and ginger as precursors, and used for the detection of thrombin and its inhibitor based on the inner filter effect (IFE).

Multipedal DNA Walker Biosensors Based on Catalyzed Hairpin Assembly and Isothermal Strand-Displacement Polymerase Reaction for the Chemiluminescent Detection of Proteins

In this study, two kinds of sensitive biosensors based on a multipedal DNA walker along a three-dimensional DNA functional magnet particles track for the chemiluminescent detection of streptavidin (SA) are constructed and compared. In the presence of SA, a multipedal DNA walker was constructed by a biotin-modified catalyst as a result of the terminal protection to avoid being digested by exonuclease I. Then, through a toehold-mediated strand exchange, a "leg" of a multipedal DNA walker interacted with a toehold of a catalyzed hairpin assembly (CHA)-H1 coupled with magnetic microparticles (MMPs) and opened its hairpin structure. The newly open stem in CHA-H1 was hybridized with a toehold of biotin-labeled H2. Via the strand displacement process, H2 displaced one "leg" of a multipedal DNA walker, and the other "leg" continued to interact with the neighboring H1 to initiate the next cycle. In order to solve the high background caused by the hybridization between CHA-H1 and H2 without a CHA-catalyst, the other model was designed. The principle of the other model (isothermal strand-displacement polymerase reaction (ISDPR)-DNA walker) was similar to that of the above one. After the terminal protection of SA, a "leg" of a multipedal DNA walker was triggered to open the hairpin of the ISDPR-H1 conjugated with MMPs. Then, the biotin-modified primer hybridized with the newly exposed DNA segment, triggering the polymerization reaction with the assistance of dNTPs/polymerase. As for the extension of the primer, the "leg" of a multipedal DNA walker was displaced so that the other "leg" could trigger the proximal H1 to go onto the next cycle. Due to its lower background and stronger signal, a multipedal DNA walker based on an ISDPR had a lower limit of detection for SA. The limit of detection for SA was 6.5 pM, and for expanding the application of the method, the detections of the folate receptor and thrombin were explored. In addition, these DNA walker methods were applied in complex samples successfully.

Magnetic force assisted electrochemical sensor for the detection of thrombin with aptamer-antibody sandwich formation

A magnetic force assisted electrochemical aptamer-antibody sandwich assay (MESA) was developed for the detection of thrombin as a model protein in serum samples. The MESA using the formation of sandwich complexes on the electrochemical sensor probe for reaction and the removal of unbound bioconjugates from the sensor surface without washing are controlled by a magnetic field. Thrombin was determined by the cathodic currents of a toluidine blue O (TBO) attached with thrombin antibody modified magnetic nanoparticle (MNP) at the sensor surface. To detect thrombin in a serum sample, we applied a thrombin-specific aptamer as the capture molecule bound to the functionalized conducting polymer layer (poly-(2,2´:5´,5″-terthiophene-3´-p-benzoic acid) (pTBA)), and streptavidin and starch coated-MNP was conjugated with biotinylated thrombin antibodies (Ab) and TBO as the bioconjugate (MNP@Ab-TBO). The characterization of MNP@Ab-TBO and sensor probe was performed using voltammetry, impedance spectroscopy, XPS, and UV-VIS spectroscopy. The experimental conditions were optimized in terms of pH, binding time, removal time of unbound bioconjugates, and applied potential. The dynamic ranges of thrombin were from 1.0 to 500 nM with detection limit of 0.49 ( ± 0.06) nM. The recovery test demonstrates the reliability of the proposed sensing system for a handheld device.

Aptamer-Based ELISA Assay for Highly Specific and Sensitive Detection of Zika NS1 Protein

We report here a few Zika NS1-binding ssDNA aptamers selected using the conventional SELEX protocol, and their application in an ELISA assay for sensitive diagnosis of Zika NS1 protein. Among the aptamers identified, aptamers 2 and 10 could recognize different binding epitopes of Zika NS1 protein. This complementary in binding site, when coupled with an extraordinarily high binding affinity by 2 (41-nt, K_D = 45 pM) and high specificity by 10, was used successfully to construct an ELISA-based assay where 2 and 10 serve as the capture and detection agents, respectively, giving rise to a highly specific detection of Zika NS1 with a detection limit of 100 ng/mL in buffer. Further testing of a few in-house anti-Zika NS1 antibodies show that 2 could also pair with an anti-Zika NS1 antibody. Such aptamer-antibody pairing not only lowers the detection sensitivity by 3 orders of magnitude to 0.1 ng/mL in buffer but also enable highly sensitive detection of as low as 1 and 10 ng/mL of Zika NS1 to be carried out in 10% and 100% human serum, respectively. These results suggest that the selected aptamers would be useful for medical diagnosis of Zika virus infection in various aptamer-based diagnostic devices including ELISA assay.

Mapping the affinity landscape of Thrombin-binding aptamers on 2΄F-ANA/DNA chimeric G-Quadruplex microarrays

In situ fabricated nucleic acids microarrays are versatile and very high-throughput platforms for aptamer optimization and discovery, but the chemical space that can be probed against a given target has largely been confined to DNA, while RNA and non-natural nucleic acid microarrays are still an essentially uncharted territory. 2΄-Fluoroarabinonucleic acid (2΄F-ANA) is a prime candidate for such use in microarrays. Indeed, 2΄F-ANA chemistry is readily amenable to photolithographic microarray synthesis and its potential in high affinity aptamers has been recently discovered. We thus synthesized the first microarrays containing 2΄F-ANA and 2΄F-ANA/DNA chimeric sequences to fully map the binding affinity landscape of the TBA1 thrombin-binding G-quadruplex aptamer containing all 32 768 possible DNA-to-2΄F-ANA mutations. The resulting microarray was screened against thrombin to identify a series of promising 2΄F-ANA-modified aptamer candidates with K_ds significantly lower than that of the unmodified control and which were found to adopt highly stable, antiparallel-folded G-quadruplex structures. The solution structure of the TBA1 aptamer modified with 2΄F-ANA at position T3 shows that fluorine substitution preorganizes the dinucleotide loop into the proper conformation for interaction with thrombin. Overall, our work strengthens the potential of 2΄F-ANA in aptamer research and further expands non-genomic applications of nucleic acids microarrays.

Through a Window, Brightly: A Review of Selected Nanofabricated Thin-Film Platforms for Spectroscopy, Imaging, and Detection

We present a review of the use of selected nanofabricated thin films to deliver a host of capabilities and insights spanning bioanalytical and biophysical chemistry, materials science, and fundamental molecular-level research. We discuss approaches where thin films have been vital, enabling experimental studies using a variety of optical spectroscopies across the visible and infrared spectral range, electron microscopies, and related techniques such as electron energy loss spectroscopy, X-ray photoelectron spectroscopy, and single molecule sensing. We anchor this broad discussion by highlighting two particularly exciting exemplars: a thin-walled nanofluidic sample cell concept that has advanced the discovery horizons of ultrafast spectroscopy and of electron microscopy investigations of in-liquid samples; and a unique class of thin-film-based nanofluidic devices, designed around a nanopore, with expansive prospects for single molecule sensing. Free-standing, low-stress silicon nitride membranes are a canonical structural element for these applications, and we elucidate the fabrication and resulting features-including mechanical stability, optical properties, X-ray and electron scattering properties, and chemical nature-of this material in this format. We also outline design and performance principles and include a discussion of underlying material preparations and properties suitable for understanding the use of alternative thin-film materials such as graphene.

Aptamer-Modified Semiconductor Quantum Dots for Biosensing Applications

Semiconductor quantum dots have attracted extensive interest in the biosensing area because of their properties, such as narrow and symmetric emission with tunable colors, high quantum yield, high stability and controllable morphology. The introduction of various reactive functional groups on the surface of semiconductor quantum dots allows one to conjugate a spectrum of ligands, antibodies, peptides, or nucleic acids for broader and smarter applications. Among these ligands, aptamers exhibit many advantages including small size, high chemical stability, simple synthesis with high batch-to-batch consistency and convenient modification. More importantly, it is easy to introduce nucleic acid amplification strategies and/or nanomaterials to improve the sensitivity of aptamer-based sensing systems. Therefore, the combination of semiconductor quantum dots and aptamers brings more opportunities in bioanalysis. Here we summarize recent advances on aptamer-functionalized semiconductor quantum dots in biosensing applications. Firstly, we discuss the properties and structure of semiconductor quantum dots and aptamers. Then, the applications of biosensors based on aptamer-modified semiconductor quantum dots by different signal transducing mechanisms, including optical, electrochemical and electrogenerated chemiluminescence approaches, is discussed. Finally, our perspectives on the challenges and opportunities in this promising field are provided.

Integrated Magnetic Bead-Quantum Dot Immunoassay for Malaria Detection

Malaria persists as a disease of high morbidity and mortality due to improper diagnosis, overuse of drugs, rapidly evolving drug resistant parasites, and poor disease monitoring. The two common tests used in developing countries, microscopic examination of Glemsa slides and rapid diagnostic tests (RDTs), have limitations associated with variability in specificity and sensitivity, and qualitative outcome. Here we report on an immunoassay using magnetic beads for capture and quantum dots for detection of histidine-rich protein 2 (HRP2). Conventional immunoassays, such as ELISA, and molecular analysis tools, such as PCR, are difficult to implement in low resource settings. Therefore, to provide a proof-of-principle of translation of this assay to low resource settings, we demonstrate HRP2 detection in an automated droplet-based microfluidic device. Droplet-based platforms have the potential to allow translation of molecular detection assays to point-of-care use in low resource settings.

Bioengineering Microgels and Hydrogel Microparticles for Sensing Biomolecular Targets

Hydrogels, and in particular microgels, are playing an increasingly important role in a diverse range of applications due to their hydrophilic, biocompatible, and highly flexible chemical characteristics. On this basis, solution-like environment, non-fouling nature, easy probe accessibility and target diffusion, effective inclusion of reporting moieties can be achieved, making them ideal substrates for bio-sensing applications. In fact, hydrogels are already successfully used in immunoassays as well as sensitive nucleic acid assays, also enabling hydrogel-based suspension arrays. In this review, we discuss key parameters of hydrogels in the form of micron-sized particles to be used in sensing applications, paying attention to the protein and oligonucleotides (i.e., miRNAs) targets as most representative kind of biomarkers.

Blood clot detection using magnetic nanoparticles

Deep vein thrombosis, the development of blood clots in the peripheral veins, is a very serious, life threatening condition that is prevalent in the elderly. To deliver proper treatment that enhances the survival rate, it is very important to detect thrombi early and at the point of care. We explored the ability of magnetic particle spectroscopy (MSB) to detect thrombus via specific binding of aptamer functionalized magnetic nanoparticles with the blood clot. MSB uses the harmonics produced by nanoparticles in an alternating magnetic field to measure the rotational freedom and, therefore, the bound state of the nanoparticles. The nanoparticles' relaxation time for Brownian rotation increases when bound [A.M. Rauwerdink and J. B. Weaver, Appl. Phys. Lett. 96, 1 (2010)]. The relaxation time can therefore be used to characterize the nanoparticle binding to thrombin in the blood clot. For longer relaxation times, the approach to saturation is more gradual reducing the higher harmonics and the harmonic ratio. The harmonic ratios of nanoparticles conjugated with anti-thrombin aptamers (ATP) decrease significantly over time with blood clot present in the sample medium, compared with nanoparticles without ATP. Moreover, the blood clot removed from the sample medium produced a significant MSB signal, indicating the nanoparticles are immobilized on the clot. Our results show that MSB could be a very useful non-invasive, quick tool to detect blood clots at the point of care so proper treatment can be used to reduce the risks inherent in deep vein thrombosis.

Biosensing of DNA oxidative damage: a model of using glucose meter for non-glucose biomarker detection

Non-glucose biomarker-DNA oxidative damage biomarker 8-hydroxy-2′-deoxyguanosine (8-OHdG) has been successfully detected using a smartphone-enabled glucose meter. Through a series of immune reactions and enzymatic reactions on a solid lateral flow platform, 8-OHdG concentration has been converted to a relative amount of glucose, and therefore can be detected by conventional glucose meter directly. The device was able to detect 8-OHdG concentrations in phosphate buffer saline as low as 1.73 ng mL⁻¹ with a dynamic range of 1–200 ng mL⁻¹. Considering the inherent advantages of the personal glucose meter, the demonstration of this device, therefore, should provide new opportunities for the monitoring of a wide range of biomarkers and various target analytes in connection with different molecular recognition events.

Nanoslit-concentration-chip integrated microbead-based protein assay system for sensitive and quantitative detection

A nanoslit-integrated microfluidic chip is developed as a microbead-based assay platform for the sensitive and quantitative detection of protein.

Novel multifunctionalized peryleneteracarboxylic/amine supramolecules for electrochemical assay

In this work, a series of novel multifunctionalized peryleneteracarboxylic supramolecules were synthesized based on hydrogen bonding interactions between 3,4,9,10-perylenetetracarboxylic acid (PTCA) and amines, which possess large specific surface area, good membrane-forming properties and high stability. Importantly, an interesting phenomenon was found in that these series of supramolecules could conciliate disorderly redox peaks of PTCA and result in a pair of well-defined redox peaks, which were able to act as redox carriers for charge-generation and electron-transportion. And the probable mechanism for this phenomenon was discussed for the first time in detail through the integration of theoretical with practical research. To further reveal the advantages of these novel multifunctionalized supramolecule nanomaterials, PTCA/triethylamine (PTCA/TEA) was chosen as the best candidate for a redox carrier to participate in a "signal-on" aptasensor for thrombin (TB) detection by employing Fe₃O₄ magnetic beads (MBs) as a good enzyme mimic to catalyze the PTCA/TEA for signal amplification. As a result, a wide linear detection range of 0.0001-50 nM is acquired with a relatively low detection limit of 0.05 pM. And the proposed aptasensor exhibited good specificity and acceptable reproducibility and stability. After all, the explorations between PTCA and amines would set up a meaningful basis in seeking multifunctionalized supramolecule nanomaterials based on PTCA for extending the application of PTCA in a wider range of fields, and exploring the essential reason for the referred peculiar phenomenon for PTCA.

Highly sensitive chemiluminescence biosensor for protein detection based on the functionalized magnetic microparticles and the hybridization chain reaction

An ultrasensitive chemiluminescence (CL) biosensor for the detection of protein is developed in this study based on the functionalized magnetic microparticles (MMPs) and the hybridization chain reaction (HCR). First, the primer hybridized with the thrombin aptamer conjugated on the surface of MMPs. Then the HCR was triggered by part of the primer and its products were assembled on the surface of the MMPs. Through the interaction between streptavidin and biotin, the streptavidin-horseradish peroxidase (SA-HRP) was coupled with the HCR products. In the presence of thrombin, the HCR products conjugating with SA-HRP were released from the surface of MMPs after the aptamer recognized and bound to its target molecule. So the released SA-HRP in the supernatant produced a significant chemiluminescence imaging signal after the addition of H₂O₂-luminol. The detection limit of thrombin with this method could be as low as 9.7fM. Besides, the sensing strategy was modified by changing the adding order of reagents that was then successfully applied in the detection of thrombin in complex sample. What's more, the DNA detection also could be carried out with this method, which demonstrated the universality of the proposed sensing strategy.

Lab-on-a-disc agglutination assay for protein detection by optomagnetic readout and optical imaging using nano- and micro-sized magnetic beads

We present a biosensing platform for the detection of proteins based on agglutination of aptamer coated magnetic nano- or microbeads. The assay, from sample to answer, is integrated on an automated, low-cost microfluidic disc platform. This ensures fast and reliable results due to a minimum of manual steps involved. The detection of the target protein was achieved in two ways: (1) optomagnetic readout using magnetic nanobeads (MNBs); (2) optical imaging using magnetic microbeads (MMBs). The optomagnetic readout of agglutination is based on optical measurement of the dynamics of MNB aggregates whereas the imaging method is based on direct visualization and quantification of the average size of MMB aggregates. By enhancing magnetic particle agglutination via application of strong magnetic field pulses, we obtained identical limits of detection of 25pM with the same sample-to-answer time (15min 30s) using the two differently sized beads for the two detection methods. In both cases a sample volume of only 10µl is required. The demonstrated automation, low sample-to-answer time and portability of both detection instruments as well as integration of the assay on a low-cost disc are important steps for the implementation of these as portable tools in an out-of-lab setting.

Multiphase ferrofluid flows for micro-particle focusing and separation

Ferrofluids have demonstrated great potential for a variety of manipulations of diamagnetic (or non-magnetic) micro-particles/cells in microfluidics, including sorting, focusing, and enriching. By utilizing size dependent magnetophoresis velocity, most of the existing techniques employ single phase ferrofluids to push the particles towards the channel walls. In this work, we demonstrate a novel strategy for focusing and separating diamagnetic micro-particles by using the laminar fluid interface of two co-flowing fluids-a ferrofluid and a non-magnetic fluid. Next to the microfluidic channel, microscale magnets are fabricated to generate strong localized magnetic field gradients and forces. Due to the magnetic force, diamagnetic particles suspended in the ferrofluid phase migrate across the ferrofluid stream at the size-dependent velocities. Because of the low Reynolds number and high Péclet number associated with the flow, the fluid interface is sharp and stable. When the micro-particles migrate to the interface, they are accumulated near the interface, resulting in effective focusing and separation of particles. We investigated several factors that affect the focusing and separation efficiency, including susceptibility of the ferrofluid, distance between the microfluidic channel and microscale magnet, and width of the microfluidic channel. This concept can be extended to multiple fluid interfaces. For example, a complete separation of micro-particles was demonstrated by using a three-stream multiphase flow configuration.

Real Colorimetric Thrombin Aptasensor by Masking Surfaces of Catalytically Active Gold Nanoparticles

We presented a simple, cost-effective, and ultrasensitive colorimetric approach for visually detecting thrombin by the catalytic amplification of gold nanoparticles (AuNPs) and aptamer-thrombin recognition. Thrombin can be quantified in the presence of catalytic AuNP surface by using color-change time of 4-nitrophenol. Without thrombin, yellow 4-nitrophenol can freely access the surface of AuNP and becomes colorless 4-aminophenol. With the addition of thrombin, aptamer-thrombin with large size interaction masks the partial surfaces of AuNPs, and increases the reduction time of 4-nitrophenol to 4-aminophenol. The maximum number of bound thrombin fully mask the catalytic AuNP surface, and thus 4-nitrophenol cannot approach to AuNP surface, the color of the solution remains yellow. The limit of detection (LOD) of 0.1 nM can be achieved with naked eyes. Of note, the method was further applied for the detection of thrombin in human serum samples, showing the results in agreement with those values obtained in an immobilization buffer by the colorimetric method.

Plasmonic-ELISA: expanding horizons

Convergence of localized surface plasmon resonance of metal nanoparticles with classical ELISA has emerged as a new class of immunoassays, i.e. plasmonic ELISA, enabling biocatalysis mediated ultrasensitive naked-eye detection of disease biomarkers.

Aptamer application in targeted delivery systems for diagnosis and treatment of breast cancer

In this review, we present the recent progress of aptamer application in targeted delivery systems for imaging and treatment of breast cancer.

DNA aptamer-based sandwich microfluidic assays for dual quantification and multi-glycan profiling of cancer biomarkers

Two novel sandwich-based immunoassays for prostate cancer (PCa) diagnosis are reported, in which the primary antibody for capture is replaced by a DNA aptamer. The assays, which can be performed in parallel, were developed in a microfluidic device and tested for the detection of free Prostate Specific Antigen (fPSA). A secondary antibody (Aptamer-Antibody Assay) or a lectin (Aptamer-Lectin Assay) is used to quantify, by chemiluminescence, both the amount of fPSA and its glycosylation levels. The use of aptamers enables a more reliable, selective and controlled sensing of the analyte. The dual approach provides sensitive detection of fPSA along with selective fPSA glycoprofiling, which is of significant importance in the diagnosis and prognosis of PCa, as tumor progression is associated with changes in fPSA glycosylation. With these approaches, we can potentially detect 0.5 ng/mL of fPSA and 3 ng/mL of glycosylated fPSA using Sambucus nigra (SNA) lectin, both within the relevant clinical range. The approach can be applied to a wide range of biomarkers, thus providing a good alternative to standard antibody-based immunoassays with significant impact in medical diagnosis and prognosis.

Aptamers-based sandwich assay for silver-enhanced fluorescence multiplex detection

In this work, aptamers-modified silver nanoparticles (AgNPs) were prepared as capture substrate, and fluorescent dyes-modified aptamers were synthesized as detection probes. The sandwich assay was based on dual aptamers, which was aimed to accomplish the highly sensitive detection of single protein and multiplex detection of proteins on one-spot. We found that aptamers-modified AgNPs based microarray was much superior to the aptamer based microarray in fluorescence detection of proteins. The result shows that the detection limit of the sandwich assay using AgNPs probes for thrombin or platelet-derived growth factor-BB (PDGF-BB) is 80 or 8 times lower than that of aptamers used directly. For multiplex detection of proteins, the detection limit was 625 pM for PDGF-BB and 21 pM for thrombin respectively. The sandwich assay based on dual aptamers and AgNPs was sensitive and specific.

Split aptamer mediated endonuclease amplification for small-molecule detection

A novel, highly sensitive split aptamer mediated endonuclease amplification strategy for the construction of aptameric sensors is reported.

Magnetic bead-quantum dot assay for detection of a biomarker for traumatic brain injury

Current diagnostic methods for traumatic brain injury (TBI), which accounts for 15% of all emergency room visits, are limited to neuroimaging modalities. The challenges of accurate diagnosis and monitoring of TBI have created the need for a simple and sensitive blood test to detect brain-specific biomarkers. Here we report on an assay for detection of S100B, a putative biomarker for TBI, using antibody-conjugated magnetic beads for capture of the protein, and antibody-conjugated quantum dots for optical detection. From Western Blot, we show efficient antigen capture and concentration by the magnetic beads. Using magnetic bead capture and quantum dot detection in serum samples, we show a wide detection range and detection limit below the clinical cut-off level.

Aptamer-Phage Reporters for Ultrasensitive Lateral Flow Assays

We introduce the modification of bacteriophage particles with aptamers for use as bioanalytical reporters, and demonstrate the use of these particles in ultrasensitive lateral flow assays. M13 phage displaying an in vivo biotinylatable peptide (AviTag) genetically fused to the phage tail protein pIII were used as reporter particle scaffolds, with biotinylated aptamers attached via avidin-biotin linkages, and horseradish peroxidase (HRP) reporter enzymes covalently attached to the pVIII coat protein. These modified viral nanoparticles were used in immunochromatographic sandwich assays for the direct detection of IgE and of the penicillin-binding protein from Staphylococcus aureus (PBP2a). We also developed an additional lateral flow assay for IgE, in which the analyte is sandwiched between immobilized anti-IgE antibodies and aptamer-bearing reporter phage modified with HRP. The limit of detection of this LFA was 0.13 ng/mL IgE, ∼100 times lower than those of previously reported IgE assays.