Simple and rapid colorimetric biosensors based on DNA aptamer and noncrosslinking gold nanoparticle aggregation

Aptamer Clicked Poly(ferrocenylsilanes) at Au Nanoparticles as Platforms with Multiple Function[†]

Aptamers are widely used in biosensing due to their specific sensitivity toward many targets. Thus, gold nanoparticle (AuNP) aptasensors are subject to intense research due to the complementary properties of aptamers as sensing elements and AuNPs as transducers. We present herein a novel method for the functional coupling of thrombin-specific aptamers to AuNPs via an anionic, redox-active poly(ferrocenylsilane) (PFS) polyelectroyte. The polymer acts as a co-reductant and stabilizer for the AuNPs, provides grafting sites for the aptamer, and can be used as a redox sensing element, making the aptamer-PFS-AuNP composite (aptamer-AuNP) a promising model system for future multifunctional sensors. The aptamer-AuNPs exhibit excellent colloidal stability in high ionic strength environments owing to the combined electrosteric stabilizing effects of the aptamer and the PFS. The synthesis of each assembly element is described, and the colloidal stability and redox responsiveness are studied. As an example to illustrate applications, we present results for thrombin sensitivity and specificity using the specific aptamer.

Detection of Femtomolar Amyloid-β Peptides for Early-Stage Identification of Alzheimer's Amyloid-β Aggregation with Functionalized Gold Nanoparticles

Progressive amyloid-β (Aβ) fibrillar aggregates have long been considered as the pathogenesis of Alzheimer's disease (AD). Biocompatible and stable cysteine-Aβ peptide-conjugated gold nanoparticles (Cys-Aβ@AuNP) are demonstrated as suitable materials for detecting subfemtomolar Aβ peptides in human plasma. Incubation with Aβ peptides causes the Cys-Aβ@AuNP to aggregate and changes its absorption spectra. The spectral change is especially apparent and noticeable when detecting subfemtomolar Aβ peptides, and the aggregates contain only two or three AuNPs. Cys-Aβ@AuNP can also be used to identify early-stage Aβ oligomerization, which is not possible using the conventional method, in which the fluorescence of thioflavin-T is measured. The ability to detect Aβ oligomerization can facilitate therapeutics for AD. In addition, the binding of Aβ peptides by Cys-Aβ@AuNP in combination with centrifugation redirects the conventional Aβ aggregation pathway and can effectively inhibit the formation of toxic Aβ oligomers or fibrils. Therefore, the proposed Cys-Aβ@AuNP can also be used to develop effective therapeutic agents to inhibit Aβ aggregation. The results obtained in this study are expected to open revolutionary ways to both detect and inhibit Aβ aggregation at an early stage.

Sandwich Immunosensor Based on Particle Motion: How Do Reactant Concentrations and Reaction Pathways Determine the Time-Dependent Response of the Sensor?

To control and optimize the speed of a molecular biosensor, it is crucial to quantify and understand the mechanisms that underlie the time-dependent response of the sensor. Here, we study how the kinetic properties of a particle-based sandwich immunosensor depend on underlying parameters, such as reactant concentrations and the size of the reaction chamber. The data of the measured sensor responses could be fitted with single-exponential curves, with characteristic response times that depend on the analyte concentration and the binder concentrations on the particle and substrate. By comparing characteristic response times at different incubation configurations, the data clarifies how two distinct reaction pathways play a role in the sandwich immunosensor, namely, analyte binding first to particles and thereafter to the substrate, and analyte binding first to the substrate and thereafter to a particle. For a concrete biosensor design, we found that the biosensor is dominated by the reaction pathway where analyte molecules bind first to the substrate and thereafter to a particle. Within this pathway, the binding of a particle to the substrate-bound analyte dominates the sensor response time. Thus, the probability of a particle interacting with the substrate was identified as the main direction to improve the speed of the biosensor while maintaining good sensitivity. We expect that the developed immunosensor and research methodology can be generally applied to understand the reaction mechanisms and optimize the kinetic properties of sandwich immunosensors with particle labels.

Signal amplification strategies in biosensing of extracellular vesicles (EVs)

Extracellular vesicles (EVs) are membrane-enclosed vesicles secreted from mammalian cells. EVs act as multicomponent delivery vehicles to carry a wide variety of biological molecular information and participate in intercellular communications. Since elevated levels of EVs are associated with some pathological states such as inflammatory diseases and cancers, probing circulating EVs holds a great potential for early diagnostics. To this end, several detection methods have been developed in which biosensors have attracted great attentions in identification of EVs due to their simple instrumentation, versatile design and portability for point-of-care applications. The concentrations of EVs in bodily fluids are extremely low (i.e. 1-100 per μl) at early stages of a disease, which necessitates the use of signal amplification strategies for EVs detection. In this way, this review presents and discusses various amplification strategies for EVs biosensors based on detection modalities including surface plasmon resonance (SPR), calorimetry, fluorescence, electrochemical and electrochemiluminescence (ECL). In addition, microfluidic systems employed for signal amplification are reviewed and discussed in terms of their design and integration with the detection methods.

Advances in chilling injury of postharvest fruit and vegetable: Extracellular ATP aspects

Due to the global use of cold chain, the development of postharvest technology to reduce chilling injury (CI) in postharvest fruits and vegetables during storage and transport is needed urgently. Considerable evidence shows that maintaining intracellular adenosine triphosphate (iATP) in harvested fruits and vegetables is beneficial to inhibiting CI occurrence. Extracellular ATP (eATP) is a damage-associated signal molecule and plays an important role in CI of postharvest fruits and vegetables through its receptor and subsequent signal transduction under low-temperature stress. The development of new aptasensors for the simultaneous determination of eATP level allows for better understanding of the roles of eATP in a myriad of responses mediated by low-temperature stress in relation to the chilling tolerance of postharvest fruits and vegetables. The multiple biological functions of eATP and its receptors in postharvest fruits and vegetables were attributed to interactions with reactive oxygen species (ROS) and nitric oxide (NO) in coordination with phytohormones and other signaling molecules via downstream physiological activities. The complicated interconnection among eATP in relation to its receptors, eATP/iATP homeostasis, ROS, NO, and heat shock proteins triggered by eATP recognition has been emphasized. This paper reviews recent advances in the beneficial effects of energy handling, outlines the production and homeostasis of eATP, discusses the possible mechanism of eATP and its receptors in chilling tolerance, and provides future research directions for CI in postharvest fruits and vegetables during low-temperature storage.

Gold nanoparticles (AuNP)-based aptasensor for enteropathogenic Escherichia coli detection

BACKGROUND

Diarrhea is a major cause of severe gastrointestinal illness in the infant especially in many developing countries. Although this molecular technique has been accepted as standard technique to detect Diarrhea-causing EPEC, the practical aspect of this technique for in-site rapid screening purposes is still facing a major challenge. In this study, we characterized EPEC specific aptamers and applied it as an AuNP-based aptasensor for point of care (POC) diagnosis purpose.

METHODS

As many as six selected DNA aptamers was screened using target bacteria and the bound aptamer was measured by qPCR technique. Moreover, Kd value for each optimal bound aptamer was measured by using the same technique. Colorimetry assay was applied to test specificity and LOD of AuNP-based aptasensor.

RESULTS

Two DNA aptamers have been successfully obtained to detect Enteropathogenic Escherichia coli K.1.1. DNA aptamer S8-7 exhibited constant dissociation (Kd) value of 17.08 nM, while DNA aptamer S10-5 exhibited Kd value of 34.14 nM. AuNP-based aptasensor showed high selectivity and specificity for EPEC K.1.1 with a limit of detection (LOD) value of 10⁵ CFU/mL. Truncation study on DNA aptamer S8-7 showed that elimination of primer binding sequence only slightly increased both performance of detection and LOD value of AuNP-based aptasensor.

CONCLUSION

Further study is necessary to improve AuNP-aptasensor performance such as through mutagenesis approach on targeted DNA aptamers before AuNP-based aptasensor can be applied as a biosensor in point of care (POC) diagnosis.

Polymer–Metal Composite Healthcare Materials: From Nano to Device Scale

Metals have been investigated as biomaterials for a wide range of medical applications. At nanoscale, some metals, such as gold nanoparticles, exhibit plasmonics, which have motivated researchers’ focus on biosensor development. At the device level, some metals, such as titanium, exhibit good physical properties, which could allow them to act as biomedical implants for physical support. Despite these attractive features, the non-specific delivery of metallic nanoparticles and poor tissue–device compatibility have greatly limited their performance. This review aims to illustrate the interplay between polymers and metals, and to highlight the pivotal role of polymer–metal composite/nanocomposite healthcare materials in different biomedical applications. Here, we revisit the recent plasmonic engineered platforms for biomolecules detection in cell-free samples and highlight updated nanocomposite design for (1) intracellular RNA detection, (2) photothermal therapy, and (3) nanomedicine for neurodegenerative diseases, as selected significant live cell–interactive biomedical applications. At the device scale, the rational design of polymer–metallic medical devices is of importance for dental and cardiovascular implantation to overcome the poor physical load transfer between tissues and devices, as well as implant compatibility under a dynamic fluidic environment, respectively. Finally, we conclude the treatment of these innovative polymer–metal biomedical composite designs and provide a future perspective on the aforementioned research areas.

An entropy-driven signal-off DNA circuit for label-free, visual detection of small molecules with enhanced accuracy

An entropy-driven DNA circuit offers an efficient means of sensitive analyte detection with signal amplification. In this article, we rationally engineered an aptamer-based entropy-driven signal-off DNA circuit for colorimetric detection of small molecules. The proposed signal-off DNA circuit is activated by target small molecule binding to drive the collapse of G-quadruplex DNAzyme, accompanied by the colour change of the detection solution from dark blue to light blue. Entropy-driven recycling hybridization significantly magnified the input signal of the target small molecule. Such an assay enables naked-eye detection of adenosine triphosphate and oxytetracycline at concentrations as low as 0.5 μM and 1 μM respectively. Moreover, when compared with the signal-on DNA circuit, the entropy-driven signal-off DNA circuit for colorimetric detection has two advantages. Firstly, unlike in the signal-on DNA circuit, the unavoidable formation of waste complexes in the absence of a target in the signal-off DNA circuit has no influence on target detection performance as its background signal is only determined by the substrate complex. Secondly, the signal-on DNA circuit cannot distinguish false-positive signals generated by invasive catalysts (e.g., HRP, serum, Fe₃O₄), while the signal-off DNA circuit can distinguish those signals as undesired signals. Overall, the signal-off DNA circuit affords a novel strategy for sensitive and accurate detection of small molecules.

A Versatile Multichannel Instrument for Measurement of Ratiometric Fluorescence Intensity and Phosphorescence Lifetime

Optical biosensing is being actively investigated for minimally-invasive monitoring of key biomarkers both in vitro and in vivo. However, typical benchtop instruments are not portable and are not well suited to high-throughput, real-time analysis. This paper presents a versatile multichannel instrument for measurement of emission intensity and lifetime values arising from luminescent biosensor materials. A detailed design description of the opto-electronic hardware as well as the control software is provided, elaborating a flexible, user-configurable system that may be customized or duplicated for a wide range of applications. This article presents experimental measurements that prove the in vitro and in vivo functionality of the system. Such tools may be adopted for many research and development purposes, including evaluation of new biosensor materials, and may also serve as prototypes for future miniaturized handheld or wearable devices.

Biosensors based on aptamer-conjugated gold nanoparticles: A review

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

Cascaded pattern formation in hydrogel medium using the polymerisation approach

Reaction-diffusion systems are one of the models of the formation process with various patterns found in nature. Inspired by natural pattern formation, several methods for designing artificial chemical reaction-diffusion systems have been proposed. DNA is a suitable building block to build such artificial systems owing to its programmability. Previously, we reported a line pattern formed due to the reaction and diffusion of synthetic DNA; however, the width of the line was too wide to be used for further applications such as parallel and multi-stage pattern formations. Here, we propose a novel method to programme a reaction-diffusion system in a hydrogel medium to realise a sharp line capable of forming superimposed and cascaded patterns. The mechanism of this system utilises a two-segment polymerisation of DNA caused by hybridisation. To superimpose the system, we designed orthogonal DNA sequences that formed two lines in different locations on the hydrogel. Additionally, we designed a reaction to release DNA and form a cascade pattern, in which the third line appears between the two lines. To explain the mechanism of our system, we modelled the system as partial differential equations, whose simulation results agreed well with the experimental data. Our method to fabricate cascaded patterns may inspire combinations of DNA-based technologies and expand the applications of artificial reaction-diffusion systems.

Molecular detection using aptamer-modified gold nanoparticles with an immobilized DNA brush for the prevention of non-specific aggregation

Gold nanoparticles (AuNPs) are often used for biosensing. In particular, aptamer-modified AuNPs are often used for colorimetric molecular detection, where target molecule-induced AuNP aggregates can be recognized by a color change from red to blue. However, non-specific aggregation could be induced by various compounds, leading to false-positive results. In this work we employed high-density ssDNA modification on the AuNP surface to prevent non-specific aggregation. The covalently immobilized DNA brush was used as an anchor for an aptamer specific for the target molecule. Herein, as a proof-of-concept study, we demonstrated detection of estradiol (E2), one of the endocrine-disrupting estrogen molecules as a model target, in the presence of antibiotic kanamycin (KN) as a model of co-contaminating compounds that induce non-specific aggregation of AuNPs. We also developed a smartphone dark field microscope (DFM) to visualize AuNP aggregation. Our previous study demonstrated that the observation of light scattering by AuNP aggregates with DFM can be applied for versatile molecular detection. In this work, we could successfully detect E2 with the smartphone DFM, and the results were verified by the results from a conventional benchtop DFM. This study would contribute to the future field applicability of AuNP-based sensors.

We demonstrated molecular detection using aptamer-modified gold nanoparticles with DNA-brush for the prevention of non-specific aggregation and smartphone darkfield microscopy.

GOLD SELEX: a novel SELEX approach for the development of high-affinity aptamers against small molecules without residual activity

GOLD SELEX, a novel SELEX approach has been developed that obviates the need for target immobilization for aptamer development. The approach purely relies on the affinity of the aptamers towards its target, to get detached from the gold nanoparticle (GNP) surface (weak attraction) after binding with its target. Thus, only the completely detached aptamers are selected for the next round of SELEX. This, in-process, also addresses the issue of residual binding and thus improves the sensitivity of the developed aptamers. As a proof of concept for establishing the utility of the approach for small molecules, we have developed aptamers against dichlorvos (DV), a pesticide in just 8 rounds. Using these aptamer candidates, we have developed an aptamer-NanoZyme (GNP having peroxidase mimic activity) based colorimetric assay. The developed aptamer displayed high affinity (K_d in sub micromolar range) and selectivity for DV. The developed assay could detect as low as 15 μM DV. The best-performing aptamer was also able to work in real samples like river water and commercial apple juice. The GOLD SELEX approach developed in this study, we believe, can act as a template for future SELEX strategy development and can replace the conventional SELEX strategy.

Gold nanospheres and nanorods for anti-cancer therapy: comparative studies of fabrication, surface-decoration, and anti-cancer treatments

Various gold nanoparticles have been explored as cancer therapeutics because they can be widely engineered for use as efficient drug carriers and diagnostic agents, and in photo-irradiation therapy. In the current review, we focused on shape-dependent biomedical applications of gold nanoparticles including gold nanospheres and nanorods. Fabrication and functionalization strategies of two different gold nanoparticles for anti-cancer therapy are introduced and the distinguishing performance depending on the shape is discussed to suggest the best carrier shape for specific applications. Moreover, recent advances in anti-cancer immunotherapy using gold nano-carriers are discussed. Thus, this comparative review can be helpful in deciding on suitable shapes and surface-modification strategies for preparing various gold nanoparticle-based therapeutics in anti-cancer therapy.

Laser-induced graphene interdigitated electrodes for label-free or nanolabel-enhanced highly sensitive capacitive aptamer-based biosensors

Highly porous laser-induced graphene (LIG) is easily generated in complex electrode configurations such as interdigitated electrodes (IDEs). Here, we demonstrate that their superior capacitive response at low frequencies can be exploited in affinity biosensors using thrombin aptamers as model biorecognition elements. Of specific interest was the effect of electrode surface area on capacitance detection, and the comparison between a label-free format and enhancement strategies afforded by carboxy group bearing polymeric nanoparticles or liposomes. Electrochemical impedance spectroscopy (EIS) was used to investigate the LIG performance and optimize the biosensor design. Interestingly, the label-free strategy performed extremely well and additional labels decreased the limit of detection or increased the sensitivity only minimally. It is assumed that the highly porous nature of the LIG structures dominates the capacitive response so that labels removed from the surface have only limited influence Also, while slight performance changes can be observed for smaller vs. larger electrode structures, the performance of a LIG IDE is reasonably independent of its size. In the end, a dynamic range of 5 orders of magnitude was obtained (0.01 nM-1000 nM) with a limit of detection as low as 0.12 pM. When measured in serum, this increased to 1.3 pM. The good reproducibility (relative standard deviation (RSD), 4.90%) and repeatability (RSD, 2.59%) and good long-term stability (>7 weeks at 4 °C) prove that a LIG-based capacitance sensor is an excellent choice for affinity-based biosensor. The ease-of-production, the simplicity of modification and the superior performance even in a label-free format indicate that LIG-based biosensors should be considered in point-of-care diagnostics in the future.

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.

Nanopipettes: a potential tool for DNA detection

As the information in DNA is of practical value for clinical diagnosis, it is important to develop efficient and rapid methods for DNA detection. In the past decades, nanopores have been extensively explored for DNA detection due to their low cost and high efficiency. As a sub-group of the solid-state nanopore, nanopipettes exhibit great potential for DNA detection which is ascribed to their stability, ease of fabrication and good compatibility with other technologies, compared with biological and traditional solid-state nanopores. Herein, the review systematically summarizes the recent progress in DNA detection with nanopipettes and highlights those studies dedicated to improve the performance of DNA detection using nanopipettes through different approaches, including reducing the rate of DNA translocation, improving the spatial resolution of sensing nanopipettes, and controlling DNA molecules through novel techniques. Besides, some new perspectives of the integration of nanopipettes with other technologies are reviewed.

A photo-regulated aptamer sensor for spatiotemporally controlled monitoring of ATP in the mitochondria of living cells

Fluorescent aptamer sensors have shown enormous potential for intracellular imaging of small molecule metabolites. Since metabolites distribute differently at different subcellular locations and their concentrations and locations fluctuate with time, methods are needed for spatiotemporally controlled monitoring of these metabolites. Built upon previous success in temporal control of aptamer-based sensors, we herein report an aptamer sensor containing a photocleavable linker and using DQAsomes to target mitochondria for spatiotemporally controlled monitoring of ATP in the mitochondria of living cells. The photocleavable modification on the DNA ATP aptamer sensor can prevent sensor activation before reaching mitochondria and the sensor can then be activated upon light irradiation. The sensor has a detection limit of 3.7 μM and high selectivity against other nucleotides, allowing detection of ATP concentration fluctuations in mitochondria induced by Ca²⁺ or oligomycin. This work represents the first successful delivery of a DNA aptamer sensor to mitochondria, providing a new platform for targeted delivery to subcellular organelles for monitoring energy producing processes, as well as mitochondrial dysfunction-related diseases in different cells.

A photo-regulated ATP sensor coupled with cationic DQAsomes is developed for spatiotemporally controlled imaging of ATP in the mitochondria of living cells.

Lateral flow aptasensor for progesterone: Competitive target recognition and displacement of short complementary sequences

There is a pressing need for simple and accurate analytical tools to assess the level of EDCs in environmental samples. In this work, a simple and highly sensitive competitive lateral flow assay (LFA) was developed for progesterone (P4). Gold nanoparticles (AuNPs) were functionalized with a previously isolated 60-mer aptamer for P4 and further hybridized with 8-mer complementary sequence modified with biotin. In the absence of P4, AuNP-duplexed aptamer conjugates are capture by a test line made with streptavidin. Conformational change within aptamer sequence upon target recognition causes the release of the biotinylated complementary sequence and disappearance of the colored test line. By optimizing the hybridization location of the 8-mer biotinylated sequences, the sensitivity of sensor was improved by 20-folds to achieve 5 nM detection level of P4 in buffer and spiked tap water samples. The simply fabricated sensor demonstrated a dynamic range in the lower nanomolar range and excellent selectivity against potential interfering molecules including the closely similar 17β-estradiol (E2). The sensor can be used as a fast screening tool to assess the level of P4 in water. Implementing the developed assay avoids applying laborious extraction procedures and lengthily analysis by conventional chromatography based instruments.

Aptamer and nanomaterial based FRET biosensors: a review on recent advances (2014-2019)

Fluorescence resonance energy transfer, one of the most powerful phenomena for elucidating molecular interactions, has been extensively utilized as a biosensing tool to provide accurate information at the nanoscale. Numerous aptamer- and nanomaterial-based FRET bioassays has been developed for detection of a large variety of molecules. Affinity probes are widely used in biosensors, in which aptamers have emerged as advantageous biorecognition elements, due to their chemical and structural stability. Similarly, optically active nanomaterials offer significant advantages over conventional organic dyes, such as superior photophysical properties, large surface-to-volume ratios, photostability, and longer shelf life. In this report (with 175 references), the use of aptamer-modified nanomaterials as FRET couples is reviewed: quantum dots, upconverting nanoparticles, graphene, reduced graphene oxide, gold nanoparticles, molybdenum disulfide, graphene quantum dots, carbon dots, and metal-organic frameworks. Tabulated summaries provide the reader with useful information on the current state of research in the field. Graphical abstract Schematic representation of a fluorescence resonance energy transfer-based aptamer nanoprobe in the absence and presence of a given target molecule (analyte). Structures are not drawn to their original scales.

An aptamer based aggregation assay for the neonicotinoid insecticide acetamiprid using fluorescent upconversion nanoparticles and DNA functionalized gold nanoparticles

An acetamiprid-binding aptamer (ABA), gold nanoparticles (AuNPs) and upconversion nanoparticles (UCNPs) are used in a colorimetric and fluorometric method for the ultrasensitive and selective detection of the pesticide acetamiprid. The ABA is first configured into a duplex with a complementary DNA covalently attached to AuNPs. The resulting dsDNA-functionalized AuNP probe is not stable in 0.15 M NaCl solution and aggregates. This causing the color to change from red to purple. In the presence of acetamiprid, the ABA undergoes a structural switch from a DNA duplex to an aptamer-acetamiprid complex and consequently dissociates from the AuNPs. The partially unhybridized AuNPs are stable against salt-induced aggregation and show red color. The ratio of absorbances at 524 nm (red) and 650 nm (purple blue) varies with the concentration of acetamiprid in the 0.025-10 μM concentration range. The colorimetric signal can be further amplified by introducing DNA-modified carboxylated UCNPs (silica-coated NaYF₄:Yb,Er) which display red and green fluorescence under 980 nm excitation. An inner filter effect occurs between DNA-modified UCNPs and dsDNA-modified AuNPs. The fluorometric assay is based on the measurement of the ratio of red (654 nm) and green (540 nm) fluorescence and works in the 0.025 to 1 μM acetamiprid concentration range and has a 0.36 nM detection limit (at a signal-to-noise ratio of 3). Because of the specificity of the aptamer, the assay is high selective. It was successfully used to quantify acetamiprid in contaminated real samples. Graphical abstract Schematic presentation of an upconversion fluorescent assay for acetamiprid. It involves the principle of analyte-triggered structural switch of aptamers, salt-induced AuNP aggregation, and signal amplification from UCNP.

Optical aptasensor based on silver nanoparticles for the colorimetric detection of adenosine

A new and straightforward optical sensor for the colorimetric determination of adenosine (AD) in human urine samples was developed. The sensor comprised silver nanoparticles (AgNPs) as colorimetric elements and anti-AD aptamer (AP) as a recognition probe. In a solution containing AD and high concentration of NaCl, due to the unique binding of AD with AP, the aggregated metal nanomaterials dispersed in the solution, and the color intensity of the solution was changed accordingly. The absorbance of the solution was monitored for AD quantification. The method was applicable for the determination of AD in the concentration range of 60-280 nM with the detection limit of 21 nM. The relative standard deviation ranged from 4.8 to 8.8% for six replicates. The method showed excellent selectivity toward AD checked over some probable interfering compounds. To investigate the performance of AgNPs, the analytical characteristics of the method including linear range, detection limit, selectivity, and precision were compared with those obtained by a common AuNPs-based aptasensor. The reliability of the method was further ascertained for the detection of AD in urine samples of two lung cancer patients with percentage recoveries in the range of 98-107%.

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.

Tandem blocking of PCR extension to form a single-stranded overhang for facile, visual, and ultrasensitive gene detection

In order to detect a predetermined gene in a field test, a facile, visual, and ultrasensitive approach without the need of special and expensive machines is required. In this study, a gene in the Ebola virus was targeted as an example for diagnosis. The key strategy is to incorporate molecular blockers (azobenzene-bearing moieties or thymine dimers) in tandem in one of the PCR primers and stop the polymerase extension there to form a single-stranded overhang. The PCR product was added to the dispersion of gold nanoparticles which were labelled with a probe oligonucleotide. When the Ebola virus-specific gene existed in the specimen, the oligonucleotide on the gold particles formed a double-helix with the single-stranded overhang, and thus the dispersion remained red in color. In the absence of the gene, however, the dispersion rapidly turned to blue because of nanoparticle aggregation. The difference was explicit even when the initial specimen involved only 1 copy of the gene. Accordingly, “whether the patient is infected by the virus or not” can be easily and visually judged by the naked eye.

Here we present a simple but practically useful assay for gene detection. This strategy employs the advantages of both PCR and Au colloidal science, and thus satisfactorily fulfills the factors required for Point-of-Care detection.

Gold nanoparticle-based colorimetric biosensors

Gold nanoparticles (AuNPs) provide excellent platforms for the development of colorimetric biosensors as they can be easily functionalised, displaying different colours depending on their size, shape and state of aggregation. In the last decade, a variety of biosensors have been developed to exploit the extent of colour changes as nano-particles (NPs) either aggregate or disperse, in the presence of analytes. Of critical importance to the design of these methods is that the behaviour of the systems has to be reproducible and predictable. Much has been accomplished in understanding the interactions between a variety of substrates and AuNPs, and how these interactions can be harnessed as colorimetric reporters in biosensors. However, despite these developments, only a few biosensors have been used in practice for the detection of analytes in biological samples. The transition from proof of concept to market biosensors requires extensive long-term reliability and shelf life testing, and modification of protocols and design features to make them safe and easy to use by the population at large. Developments in the next decade will see the adoption of user friendly biosensors for point-of-care and medical diagnosis as innovations are brought to improve the analytical performances and usability of the current designs. This review discusses the mechanisms, strategies, recent advances and perspectives for the use of AuNPs as colorimetric biosensors.

Using Impedance Measurements to Characterize Surface Modified with Gold Nanoparticles

With the increased practice of preventative healthcare to help reduce costs worldwide, sensor technology improvement is vital to patient care. Point-of-care (POC) diagnostics can reduce time and lower labor in testing, and can effectively avoid transporting costs because of portable designs. Label-free detection allows for greater versatility in the detection of biological molecules. Here, we describe the use of an impedance-based POC biosensor that can detect changes in the surface modification of a micro-fabricated chip using impedance spectroscopy. Gold nanoparticles (GNPs) have been employed to evaluate the sensing ability of our new chip using impedance measurements. Furthermore, we used impedance measurements to monitor surface functionalization progress on the sensor's interdigitated electrodes (IDEs). Electrodes made from aluminum and gold were employed and the results were analyzed to compare the impact of electrode material. GNPs coated with mercaptoundecanoic acid were also used as a model of biomolecules to greatly enhance chemical affinity to the silicon substrate. The portable sensor can be used as an alternative technology to ELISA (enzyme-linked immunosorbent assays) and polymerase chain reaction (PCR)-based techniques. This system has advantages over PCR and ELISA both in the amount of time required for testing and the ease of use of our sensor. With other techniques, larger, expensive equipment must be utilized in a lab environment, and procedures have to be carried out by trained professionals. The simplicity of our sensor system can lead to an automated and portable sensing system.

Defining the copper binding aptamotif and aptamer integrated recovery platform (AIRP)

The potential copper binding sites in aptamers have been predicted on the basis of secondary structures and the binding affinity of aptamers with copper. Out of the 4 aptamers (Cu-A1 to Cu-A4) selected by SELEX and examined in the present study, the Cu-A2 aptamer shows the highest binding affinity to copper with the lowest K_D value of 1.83 × 10^-11 M. In order to confirm the binding of copper to the proposed region, the binding affinity was experimentally validated using mutation and deletion analysis. We have confirmed that the high G-C pairing patterns and short stem-interval distance play important roles in copper binding. Aptamer specificity was also verified against diverse heavy metals. We also demonstrate an Aptamer Integrated Recovery Platform (AIRP) to recover copper from acidic mine drainage. AIRP can be easily regenerated at least 20 times without significant deterioration of the retrieval performance. To the best of our knowledge, AIRP is the first demonstration of copper specific recovery using aptamers. This can be scaled up and would have diverse applications in metal contaminated water treatment, recovery and as a potential biosensor for environmental analysis, monitoring, and risk assessment.

An enzyme-free colorimetric assay using hybridization chain reaction amplification and split aptamers

A novel unmodified gold nanoparticle (AuNP)-based colorimetric assay was demonstrated using split aptamers and the hybridization chain reaction (HCR) amplification strategy. Here, the aptamer was divided into a structure-switching hairpin probe (DNA probe H1 (or H1')) and a single-stranded probe (DNA probe H2 (or H2')). In the presence of the target, DNA probe H1 (or H1') could specifically capture the target with the assistance of DNA probe H2 (or H2') to form a stable complex. Subsequently, the hairpin structure of DNA probe H1 (or H1') was changed, and then a chain reaction of hybridization events between two other hairpin probes (H3 and H4) propagated, resulting in the formation of nicked double-helices. Since it was difficult for such nicked double-helices to inhibit salt-induced AuNP aggregation, a red-to-blue color change was observed. With the elegant amplification effect of HCR, this assay showed a low detection limit (15 nM for Hg(2+) and 1 μM for adenosine), which was lower than or at least comparable to previous AuNP-based methods. The novel strategy not only eliminated the requirements of enzymatic reactions, separation processes, chemical modifications, and sophisticated instruments, but also could be used for other targets only by simply changing the DNA probe sequences.

Optical Aptasensors for Adenosine Triphosphate

Nucleic acids are among the most researched and applied biomolecules. Their diverse two- and three-dimensional structures in conjunction with their robust chemistry and ease of manipulation provide a rare opportunity for sensor applications. Moreover, their high biocompatibility has seen them being used in the construction of in vivo assays. Various nucleic acid-based devices have been extensively studied as either the principal element in discrete molecule-like sensors or as the main component in the fabrication of sensing devices. The use of aptamers in sensors - aptasensors, in particular, has led to improvements in sensitivity, selectivity, and multiplexing capacity for a wide verity of analytes like proteins, nucleic acids, as well as small biomolecules such as glucose and adenosine triphosphate (ATP). This article reviews the progress in the use of aptamers as the principal component in sensors for optical detection of ATP with an emphasis on sensing mechanism, performance, and applications with some discussion on challenges and perspectives.

DNA module platform for developing colorimetric aptamer sensors

Here we present a DNA module platform for developing simple aptamer sensors based on a microarray format combined with secondary structure prediction in silico. The platform comprises four parts: (i) aptamer, (ii) joint module, (iii) terminal stem, and (iv) a DNAzyme that catalyzes a redox reaction controlled by a structural change induced by aptamer/target binding. First, we developed a joint module, capable of sensing a conformational change in the aptamer region, that was linked to the signal transmission activity of a DNAzyme as the reporter in a concentration-dependent manner with the AMP aptamer. This module design was then used to generate an arginine sensor simply by replacing the AMP aptamer region with a previously reported arginine aptamer. Using this DNA module platform, we were also able to customize a microarray containing >10,000 sequences designed by in silico secondary structure prediction and successfully identify a new aptamer against patulin. Our results show that the DNA module platform can be used to readily devise sensors based on known aptamers as well as create new aptamer sensors by array-based screening.

Highly Hybridizable Spherical Nucleic Acids by Tandem Glutathione Treatment and Polythymine Spacing

Gold nanoparticle (AuNP)-templated spherical nucleic acids (SNAs) have been demonstrated as an important functional material in bionanotechnology. Fabrication of SNAs having high hybridization capacity to their complementary sequences is critical to ensure their applicability in areas such as antisense gene therapy and cellular sensing. The traditional salt-aging procedure is effective but tedious, requiring 1-3 days to complete. The rapid low-pH assisted protocol is efficient, but causes concerns related to nonspecific DNA adsorption to the AuNP core. To address these issues, we systematically compared the SNAs prepared by these two methods (salt-aging method and low-pH protocol). In terms of the number of complementary DNA that each SNA can bind and the average binding affinity of each thiolated DNA probe to its complementary strand, both methods yielded comparable hybridizability, although higher loading capacity was witnessed with SNAs made using the low-pH method. Additionally, it was found that nonspecific DNA binding could be eliminated almost completely by a simple glutathione (GSH) treatment of SNAs. Compared to conventional methods using toxic mercapto-hexanol or alkanethiols to remove nonspecific DNA adsorption, GSH is mild, cost-effective, and technically easy to use. In addition, GSH-passivated SNAs minimize the toxicity concerns related to AuNP-induced GSH depletion and therefore offer a more biocompatible alternative to previously reported SNAs. Moreover, rational design of probe sequences through inclusion of a polythymine spacer into the DNA sequences resulted in enhanced DNA loading capacity and stability against salt-induced aggregation. This work provides not only efficient and simple technical solutions to the issue of nonspecific DNA adsorption, but also new insights into the hybridizability of SNAs.

Aptamers: The "evolution" of SELEX

It has been more than two decades since the first aptamer molecule was discovered. Since then, aptamer molecules have gain much attention in the scientific field. This increasing traction can be attributed to their many desirable traits, such as 1) their potentials to bind a wide range of molecules, 2) their malleability, and 3) their low cost of production. These traits have made aptamer molecules an ideal platform to pursue in the realm of pharmaceuticals and bio-sensors. Despite the broad applications of aptamers, tedious procedure, high resource consumption, and limited nucleobase repertoire have hindered aptamer in application usage. To address these issues, new innovative methodologies, such as automation and single round SELEX, are being developed to improve the outcomes and rates in which aptamers are discovered.

Biomedical Applications of DNA-Conjugated Gold Nanoparticles

Gold nanoparticles (AuNPs) are useful for diagnostic and biomedical applications, mainly because of their ease in preparation and conjugation, biocompatibility, and size-dependent optical properties. However, bare AuNPs do not possess specificity for targets. AuNPs conjugated with DNA aptamers offer specificity for various analytes, such as proteins and small molecules/ions. Although DNA aptamers themselves have therapeutic and target-recognizing properties, they are susceptible to degradation in vivo. When DNA aptamers are conjugated to AuNPs, their stability and cell uptake efficiency both increase, making aptamer-AuNPs suitable for biomedical applications. Additionally, drugs can be efficiently conjugated with DNA aptamer-AuNPs to further enhance their therapeutic efficiency. This review focuses on the applications of DNA aptamer-based AuNPs in several biomedical areas, including anticoagulation, anticancer, antibacterial, and antiviral applications.

Aptamers in analytics

Nucleic acid aptamers are promising alternatives to antibodies in analytics. They are generally obtained through an iterative SELEX protocol that enriches a population of synthetic oligonucleotides to a subset that can recognize the chosen target molecule specifically and avidly. A wide range of targets is recognized by aptamers. Once identified and optimized for performance, aptamers can be reproducibly synthesized and offer other key features, like small size, low cost, sensitivity, specificity, rapid response, stability, and reusability. This makes them excellent options for sensory units in a variety of analytical platforms including those with electrochemical, optical, and mass sensitive transduction detection. Many novel sensing strategies have been developed by rational design to take advantage of the tendency of aptamers to undergo conformational changes upon target/analyte binding and employing the principles of base complementarity that can drive the nucleic acid structure. Despite their many advantages over antibodies, surprisingly few aptamers have yet been integrated into commercially available analytical devices. In this review, we discuss how to select and engineer aptamers for their identified application(s), some of the challenges faced in developing aptamers for analytics and many examples of their reported successful performance as sensors in a variety of analytical platforms.

Development of a luminescent G-quadruplex-selective iridium(III) complex for the label-free detection of adenosine

A panel of six luminescent iridium(III) complexes were synthesized and evaluated for their ability to act as G-quadruplex-selective probes. The novel iridium(III) complex 1 was found to be highly selective for G-quadruplex DNA, and was employed for the construction of a label-free G-quadruplex-based adenosine detection assay in aqueous solution. Two different detection strategies were investigated for adenosine detection, and the results showed that initial addition of adenosine to the adenosine aptamer gave superior results. The assay exhibited a linear response for adenosine in the concentration range of 5 to 120 μM (R(2) = 0.992), and the limit of detection for adenosine was 5 μM. Moreover, this assay was highly selective for adenosine over other nucleosides, and exhibited potential use for biological sample analysis.

Naked-eye nanobiosensor for therapeutic drug monitoring of methotrexate

Sensing of methotrexate at clinically-relevant concentrations was achieved with a plasmon-coupling assay.

Gold-Coated Superparamagnetic Nanoparticles for Single Methyl Discrimination in DNA Aptamers

Au- and iron-based magnetic nanoparticles (NPs) are promising NPs for biomedical applications due to their unique properties. The combination of a gold coating over a magnetic core puts together the benefits from adding the magnetic properties to the robust chemistry provided by the thiol functionalization of gold. Here, the use of Au-coated magnetic NPs for molecular detection of a single methylation in DNA aptamer is described. Binding of α-thrombin to two aptamers conjugated to these NPs causes aggregation, a phenomenon that can be observed by UV, DLS and MRI. These techniques discriminate a single methylation in one of the aptamers, preventing aggregation due to the inability of α-thrombin to recognize it. A parallel study with gold and ferromagnetic NPs is detailed, concluding that the Au coating of FexOy NP does not affect their performance and that they are suitable as complex biosensors. These results prove the high detection potency of Au-coated SPIONs for biomedical applications especially for DNA repair detection.

Non-enzymatic detection of urea using unmodified gold nanoparticles based aptasensor

Biosensing nitrogenous compounds like urea is required to control the incidents of Economically Motivated Adulteration (EMA). In this study, we report the FluMag Systematic Evolution of Ligands by Exponential Enrichment (FluMag-SELEX) method to isolate a urea specific DNA aptamer with a dissociation constant (Kd) of 232 nM. The interaction of DNA aptamer with urea has been confirmed by affinity assay, CD analysis, melting curve analysis and truncation studies. Unlike other urea sensing methods reported so far, using this urea aptamer, we demonstrate a simple, 'non-enzymatic' easy-to-use, dual readout aptasensor that exploits unmodified gold nanoparticles (AuNPs) to transduce the signals of aptamer binding to urea in terms of intrinsic fluorescence differences and color changes simultaneously. This method is free from complicated sample processing and labeling steps. The urea aptasensor displays high selectivity for urea and is free from interference from common milk adulterants. The developed aptasensor reliably detects urea adulteration in milk. The response signals linearly correlate with the increasing concentrations of urea in milk ranging from 20mM to 150 mM with detection limit of 20mM. We also show that this aptasensor can also be used as a simple fluorescence based "turn-on" sensor. The results obtained in this study are comparable to the commercial urease based detection methods.

Simultaneous direct detection of Shiga-toxin producing Escherichia coli (STEC) strains by optical biosensing with oligonucleotide-functionalized gold nanoparticles

A simultaneous direct detection of Shiga-toxin producing strains of E. coli (STEC; "Big Six" - O26, O45, O103, O111, O121, and O145) as well as O157 strains by optical biosensing with oligonucleotide-functionalized gold nanoparticles (AuNPs) was developed. Initially, conserved regions of stx genes were amplified by asymmetric polymerase chain reaction (asPCR). Pairs of single stranded thiol-modified oligonucleotides (30-mer) were immobilized onto AuNPs and used as probes to capture regions of stx1 (119-bp) and/or stx2 (104-bp) genes from STEC strains. DNA samples from pure cultures and food samples were sandwich hybridized with AuNP-oligo probes at optimal conditions (50 °C, 30 min). A complex was formed from the hybridization of AuNP-probes and target DNA fragments that retained the initial red color of the reaction solutions. For non-target DNA, a color change from red to purplish-blue was observed following an increase in salt concentration, thus providing the basis of simultaneous direct colorimetric detection of target DNA in the samples. Enrichment and pooling systems were incorporated to efficiently process a large number of food samples (ground beef and blueberries) and detection of live targets. The detection limit was <1 log CFU g(-1), requiring less than 1 h to complete after DNA sample preparation with 100% specificity. Gel electrophoresis verified AuNP-DNA hybridization while spectrophotometric data and transmission electron microscope (TEM) images supported color discrimination based on the occurrence of molecular aggregation. In conclusion, the significant features of this approach took advantage of the unique colorimetric properties of AuNPs as a low-cost and simple approach yet with high specificity for simultaneous detection of STEC strains.

Understanding aggregation-based assays: nature of protein corona and number of epitopes on antigen matters

In this study, we systematically examine how the nature of the protein corona on NPs, formed from either antibody or antigen, and how the number of binding sites or epitopes on the antigen affect aggregation.

Safety issues and new rapid detection methods in traditional Chinese medicinal materials

The safety of traditional Chinese medicine (TCM) is a major strategic issue that involves human health. With the continuous improvement in disease prevention and treatment, the export of TCM and its related products has increased dramatically in China. However, the frequent safety issues of Chinese medicine have become the 'bottleneck' impeding the modernization of TCM. It was proved that mycotoxins seriously affect TCM safety; the pesticide residues of TCM are a key problem in TCM international trade; adulterants have also been detected, which is related to market circulation. These three factors have greatly affected TCM safety. In this study, fast, highly effective, economically-feasible and accurate detection methods concerning TCM safety issues were reviewed, especially on the authenticity, mycotoxins and pesticide residues of medicinal materials.