Adenosine detection by using gold nanoparticles and designed aptamer sequences

Rapid Apta-Chromogenic Detection Method for Nitrofuran Metabolite Determination

Nitrofuran (NF) contamination in food products is a global problem resulting in the banned utilization and importation of nitrofuran contaminated products. A novel chromogenic detection method using a specific DNA aptamer with high affinity and specificity to nitrofurans was developed. Single-stranded DNA aptamers specific to nitrofuran metabolites, including 3-amino-2-oxazolidinone (AOZ), 3-amino-5-methylmorpholino-2-oxazolidinone (AMOZ), and 1-aminohydantoin (AHD), were isolated using magnetic bead-SELEX. The colorimetric detection of nitrofurans using gold nanoparticles (AuNPs) exhibited an AOZ detection range of 0.01-0.06 ppb with a limit of detection (LOD) of 0.03 ppb. At the same time, this system could detect AMOZ and AHD at a range of 0.06 ppb and 10 ppb, respectively. The fast nitrofuran extraction method was optimized for food, such as fish tissues and honey, adjusted to be completed within 3-6 h. This novel apta-chromogenic detection method could detect NF metabolites with a sensitivity below the minimum required performance limit (MPRL). This analysis will be valuable for screening, with a shortened time of detection for aquaculture products such as shrimp and fish muscle tissues.

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.

Development of "Smart Foods" for health by nanoencapsulation: Novel technologies and challenges

Importance of nanotechnology may be seen by penetration of its application in diverse areas including the food sector. With investigations and advancements in nanotechnology, based on feedback from these diverse areas, ease, and efficacy are also increasing. The food sector may use nanotechnology to encapsulate smart foods for increased health, wellness, illness prevention, and effective targeted delivery. Such nanoencapsulated targeted delivery systems may further add to the economic and nutritional properties of smart foods like stability, solubility, effectiveness, safeguard against disintegration, permeability, and bioavailability of smart/bioactive substances. But in the way of application, the fabrication of nanomaterials/nanostructures has several challenges which range from figuring out the optimal technique for obtaining them to determining the most suitable form of nanostructure for a bioactive molecule of interest. This review precisely addresses concepts, recent advances in fabrication techniques as well as current challenges/glitches of nanoencapsulation with special reference to smart foods/bioactive components. Since dealing with food materials also raises the quest for safety and regulatory norms a brief overview of the safety and regulatory aspects of nanomaterials/nanoencapsulation is also presented.

Light-up split aptamers: binding thermodynamics and kinetics for sensing

Due to their programmable structures, many aptamers can be readily split into two halves while still retaining their target binding function. While split aptamers are prevalent in the biosensor field, fundamental studies of their binding are still lacking. In this work, we took advantage of the fluorescence enhancement property of a new aptamer named OTC5 that can bind to tetracycline antibiotics to compare various split aptamers with the full-length aptamer. The split aptamers were designed to have different stem lengths. Longer stem length aptamers showed similar dissociation constants (Kd) to the full-length aptamer, while a shorter stem construct showed an 85-fold increase in Kd. Temperature-dependent fluorescence measurements confirmed the lower thermostability of split aptamers. Isothermal titration calorimetry indicated that split aptamer binding can release more heat but have an even larger entropy loss. Finally, a colorimetric biosensor using gold nanoparticles was designed by pre-assembling two thiolated aptamer halves, which can then link gold nanoparticles to give a red-to-blue color change.

Thiolate DNAzymes on Gold Nanoparticles for Isothermal Amplification and Detection of Mesothelioma-derived Exosomal PD-L1 mRNA

Catalytic DNAzymes have been used for isothermal amplification and rapid detection of nucleic acids, holding the potential for point-of-care testing applications. However, when Subzymes (universal substrate and DNAzyme) are tethered to the polystyrene magnetic microparticles via biotin-streptavidin bonds, the residual free Subzymes are often detached from the microparticle surface, which causes a significant degree of false positives. Here, we attached dithiol-modified Subzyme to gold nanoparticle and improved the limit of detection (LoD) by 200 times compared to that using magnetic microparticles. As a proof of concept, we applied our new method for the detection of exosomal programed cell-death ligand 1 (PD-L1) RNA. As the classical immune checkpoint, molecule PD-L1, found in small extracellular vesicles (sEVs, traditionally called exosomes), can reflect the antitumor immune response for predicting immunotherapy response. We achieved the LoD as low as 50 fM in detecting both the RNA homologous to the PD-L1 gene and exosomal PD-L1 RNAs extracted from epithelioid and nonepithelioid subtypes of mesothelioma cell lines, which only takes 8 min of reaction time. As the first application of isothermal DNAzymes for detecting exosomal PD-L1 RNA, this work suggests new point-of-care testing potentials toward clinical translations.

DNA-Crosslinked 2D Photonic Crystal Hydrogels for Detection of Adenosine Actuated by an Adenosine-Binding Aptamer

There is a need to develop versatile sensing motifs that can be used to detect a variety of chemical targets in resource-limited settings, for example, at the point of care. While numerous sensing technologies have been developed toward this effort, these technologies can be overly complex and require a skilled technician, extensive sample preparation, or sophisticated instrumentation to use, limiting their generalizability and application in resource-limited settings. Here, we report a novel sensing motif that utilizes DNA-crosslinked two-dimensional photonic crystal (2DPC) hydrogels. These hydrogel sensors contain a DNA aptamer recognition group that binds a target analyte. As proof of concept, we fabricated 2DPC hydrogels using a well-studied adenosine-binding aptamer. This adenosine aptamer is duplexed with a partially complementary strand and forms responsive crosslinks in the hydrogel polymer network. When adenosine is introduced, aptamer-adenosine binding occurs, breaking the DNA crosslinks and causing the hydrogel to swell. This in turn increases the particle spacing of an embedded 2DPC array, shifting the 2DPC Bragg diffraction. Thus, adenosine concentration can be monitored through 2DPC Bragg diffraction measurements. A linear range of 20 μM to 2 mM was observed. The detection limits were calculated to be 13.9 μM in adenosine-binding buffer and 26.7 μM in fetal bovine serum. This reported sensing motif has a readout that is simple and rapid and requires minimal equipment. We hypothesize that this sensing motif is generalizable and that other sensors can be easily fabricated by simply exchanging the aptamer that serves as a molecular recognition group.

Nanoarchitectonics for Abused-Drug Biosensors

Rapid, accessible, and highly accurate biosensors for the detection of addictive and abused drugs are needed to reduce the adverse personal and societal impacts of addiction. Modern sensors that utilize next-generation technologies, e.g., nanobiotechnology and nanoarchitectonics, have triggered revolutionary progress in the field as they allow accurate detection and tracking of trace levels of major classes of drugs. This paper reviews advances in the field of biosensors for the detection of commonly abused drugs, both prescribed such as codeine and morphine, and illegal narcotics like cocaine.

Comparison of Duplex and Quadruplex Folding Structure Adenosine Aptamers for Carbon Nanotube Field Effect Transistor Aptasensors

Carbon nanotube field effect transistor (CNT FET) aptasensors have been investigated for the detection of adenosine using two different aptamer sequences, a 35-mer and a 27-mer. We found limits of detection for adenosine of 100 pM and 320 nM for the 35-mer and 27-mer aptamers, with dissociation constants of 1.2 nM and 160 nM, respectively. Upon analyte recognition the 35-mer adenosine aptamer adopts a compact G-quadruplex structure while the 27-mer adenosine aptamer changes to a folded duplex. Using the CNT FET aptasensor platform adenosine could be detected with high sensitivity over the range of 100 pM to 10 µM, highlighting the suitability of the CNT FET aptasensor platform for high performance adenosine detection. The aptamer restructuring format is critical for high sensitivity with the G-quadraplex aptasensor having a 130-fold smaller dissociation constant than the duplex forming aptasensor.

Melting Curve Analysis of Aptachains: Adenosine Detection with Internal Calibration

Small molecules are ubiquitous in nature and their detection is relevant in various domains. However, due to their size, sensitive and selective probes are difficult to select and the detection methods are generally indirect. In this study, we introduced the use of melting curve analysis of aptachains based on split-aptamers for the detection of adenosine. Aptamers, short oligonucleotides, are known to be particularly efficient probes compared to antibodies thanks to their advantageous probe/target size ratio. Aptachains are formed from dimers with dangling ends followed by the split-aptamer binding triggered by the presence of the target. The high melting temperature of the dimers served as a calibration for the detection/quantification of the target based on the height and/or temperature shift of the aptachain melting peak.

Analyzing Criteria Affecting the Functionality of G-Quadruplex-Based DNA Aptazymes as Colorimetric Biosensors and Development of Quinine-Binding Aptazymes

A DNA aptazyme consists of an aptamer domain and a DNAzyme module, in which the DNAzyme activity can be regulated by the aptamer-target interaction. The complex of G-quadruplex (GQ) and hemin is a peroxidase-mimicking DNAzyme and has become increasingly popular as a reporter system for biosensing applications. The development of GQ-based aptazymes is of high interest as they can be used as label-free biosensors for the real-time detection of pathogens. Herein, we rationally designed ca. 200 GQ-based aptazyme candidates and evaluated the suitability of 14 aptamers targeting quinine, Protein A, Staphylococcus enterotoxin B, and ATP for this detection concept. As a result, six novel aptazymes were developed for the specific detection of quinine based on two quinine-binding aptamers. The rest of designed probes, however, hardly showed significant functionality. To uncover the reasons, we performed enzyme-linked oligonucleotide assays to find how the affinity of aptamers is affected once conjugated to the DNAzyme sequence or upon integration into the aptazyme probe. Furthermore, we investigated the impact of the structure-switching functionality in the parent aptamer and the effect of the reaction matrix on the efficiency of probes.

Logic Gates Based on DNA Aptamers

DNA bio-computing is an emerging trend in modern science that is based on interactions among biomolecules. Special types of DNAs are aptamers that are capable of selectively forming complexes with target compounds. This review is devoted to a discussion of logic gates based on aptamers for the purposes of medicine and analytical chemistry. The review considers different approaches to the creation of logic gates and identifies the general algorithms of their creation, as well as describes the methods of obtaining an output signal which can be divided into optical and electrochemical. Aptameric logic gates based on DNA origami and DNA nanorobots are also shown. The information presented in this article can be useful when creating new logic gates using existing aptamers and aptamers that will be selected in the future.

Fast Adhesion of Gold Nanoparticles (AuNPs) to a Surface Using Starch Hydrogels for Characterization of Biomolecules in Biosensor Applications

Gold nanoparticles (AuNPs) are the most thoroughly studied nanoparticles because of their remarkable optical properties. Color changes in assays that use AuNPs can be easily observed with the naked eye, resulting in sensitive colorimetric methods, useful for detecting a variety of biological molecules. However, while AuNPs represent an excellent nano-platform for developing analytical methods for biosensing, there are still challenges that must be overcome before colloidal AuNPs formulation can be successfully translated into practical applications. One of those challenges is the ability to immobilize AuNPs in a solid support. There are many difficulties with controlling both the cluster size and the adhesion of the coatings formed. In addition, many of the techniques employed are expensive and time-consuming, or require special equipment. Thus, a simple and inexpensive method that only requires common lab equipment for immobilizing AuNPs on a surface using Starch Hydrogels has been developed. Starch hydrogels confer a 400% increase in stability to the nanoparticles when exposed to changes in the environment while also allowing for macromolecules to interact with the AuNPs surface. Several starch derivatives were tested, including, dextrin, beta-cyclodextrin and maltodextrin, being dextrin the one that conferred the highest stability. As a proof-of-concept, a SlipChip microfluidic sensor scheme was developed to measure the concentration of DNA in a sample. The detection limit of our biosensor was found to be 25 ng/mL and 75 ng/mL for instrument and naked eye detection, respectively.

A rapid, easy, and sensitive method for detecting His-tag-containing chitinase based on ssDNA aptamers and gold nanoparticles

Chitooligosaccharides are oligosaccharides with many biological activities that can be used in food production for sweeteners, preservatives and humectants, among other products. Chitin, a long-chain polymer of N-acetylglucosamine and a derivative of glucose, can be hydrolyzed by applying chitinase to break down glycosidic bonds to form chitooligosaccharides. Chitinases arising from heterologous gene expression are usually linked to a 6 × His-tag to facilitate easy purification. Heterologously expressed chitinase linked to a 6 × His-tag is a transgenic element, but enzyme activity tests cannot be used to distinguish transgenic elements from natural elements. In this study, we established a rapid and easy method to detect His-tag-containing chitinase using gold nanoparticles (AuNPs) and ssDNA aptamers. Using this method, His-tag-containing chitinase could be detected at concentrations as low as 0.136 nM within 5 min. Color changes of AuNPs showed a positive correlation with His-tag-containing chitinase concentrations.

A novel portable biosensor based on aptamer functionalized gold nanoparticles for adenosine detection

Adenosine has received great attentions acting as a potential biomarker for monitoring lung cancer. Most of the reported studies for adenosine detection require large instruments and complicated procedures. Herein, a sensitive, rapid and in-situ colorimetric aptasensor was developed for adenosine detection. Moreover, a homemade biomimetic electronic-eye (E-eye) was established and utilized as a portable in-time detection equipment. The entire measurement can be completed within 20 min, including the combination of aptamer with adenosine or AuNPs and the detection of adenosine. Four different kinds of aptamer were compared and the results showed that the AuNPs-aptamer-biotin system was the most stable and with the widest detection range of 5.0 μM-60.0 μM and the lowest LOD of 0.17 μM. Moreover, the artificial urine samples were also tested with a linear range from 5.0 to 50.0 μM and a LOD of 0.48 μM. The results validated that the aptasensor together with the E-eye can be a promising platform for adenosine detection.

Splitting aptamers and nucleic acid enzymes for the development of advanced biosensors

In analogy to split-protein systems, which rely on the appropriate fragmentation of protein domains, split aptamers made of two or more short nucleic acid strands have emerged as novel tools in biosensor set-ups. The concept relies on dissecting an aptamer into a series of two or more independent fragments, able to assemble in the presence of a specific target. The stability of the assembled structure can further be enhanced by functionalities that upon folding would lead to covalent end-joining of the fragments. To date, only a few aptamers have been split successfully, and application of split aptamers in biosensing approaches remains as promising as it is challenging. Further improving the stability of split aptamer target complexes and with that the sensitivity as well as efficient working modes are important tasks. Here we review functional nucleic acid assemblies that are derived from aptamers and ribozymes/DNAzymes. We focus on the thrombin, the adenosine/ATP and the cocaine split aptamers as the three most studied DNA split systems and on split DNAzyme assemblies. Furthermore, we extend the subject into split light up RNA aptamers used as mimics of the green fluorescent protein (GFP), and split ribozymes.

An in-tube aptamer/gold nanoparticles coated capillary solid-phase microextraction for separation of adenosine in serum and urine samples

As an endogenous nucleoside, adenosine was significant for the diagnosis and treatment of some diseases, such as schizophrenia. However, due to the complicated matrix interference, it was difficult to monitor trace or ultra-trace adenosine directly in bio-samples. In this contribution, a novel in-tube SPME technique based on aptamer/Au nanoparticles coated open tubular fused-silica capillary was established to separate and enrich adenosine in bio-samples with high affinity. Therefore, a uniform and dense AuNPs layer was coated on the inner surface of the open tubular capillary, and then adenosine aptamer was immobilized on AuNPs with a high capacity of 2.44 μg per 27-cm capillary. As a result, the capillary shown high selectivity to adenosine with a selectivity factor of 14.4 when compared with the scrambled aptamer/AuNPs coated capillary. Also, the extraction amount of adenosine was 2.8-24.8 times higher than those of its structural analogs and contrast, such as guanosine, uridine, cytidine, thymidine, and toluic acid. After the optimization of extraction conditions, the aptamer/AuNPs coated in-tube SPME-HPLC method was developed for the adenosine assay with the linear range of 0.002-0.100 μg mL^-1 and the detection limit of 0.45 ng mL^-1. Subsequently, the approach was applied for trace adenosine monitoring in human serum and urine samples. It showed a strong performance of reducing matrix interference and improving sensitivity, and the spiking recoveries of 89.9-92.6% and 91.1-94.5% were achieved respectively.

A Bottom-Up Approach for Developing Aptasensors for Abused Drugs: Biosensors in Forensics

Aptamer-based point-of-care (POC) diagnostics platforms may be of substantial benefit in forensic analysis as they provide rapid, sensitive, user-friendly, and selective analysis tools for detection. Aptasensors have not yet been adapted commercially. However, the significance of the applications of aptasensors in the literature exceeded their potential. Herein, in this review, a bottom-up approach is followed to describe the aptasensor development and application procedure, starting from the synthesis of the corresponding aptamer sequence for the selected analyte to creating a smart surface for the sensitive detection of the molecule of interest. Optical and electrochemical biosensing platforms, which are designed with aptamers as recognition molecules, detecting abused drugs are critically reviewed, and existing and possible applications of different designs are discussed. Several potential disciplines in which aptamer-based biosensing technology can be of greatest value, including forensic drug analysis and biological evidence, are then highlighted to encourage researchers to focus on developing aptasensors in these specific areas.

Colorimetric adenosine assay based on the self-assembly of aptamer-functionalized gold nanorods

A colorimetric method is presented for ultrasensitive determination of adenosine. The assay is based on side-by-side self-assembly of aptamer-functionalized gold nanorods (Au NRs). It relies on the fact that the conjugation of the helper DNA predominantly occurs at the terminal ends of the Au NRs rather than at their sides. The adenosine aptamers consist of two pieces of ssDNA (termed C1 and C2) that were individually attached to the sides of Au NRs. In the presence of adenosine, it will be captured by C1 and C2 to form a stable sandwich structure. As a result, a side-to-side assembly of the Au NRs occurs. If the adenosine concentration is increased, the absorbance of the Au NRs at 742 nm gradually decreases, and the color changes from brick red to dark brown. Response is linear range in the 10 pM to 5 nM adenosine concentration range, and the detection limit is as low as 3.3 pM. Adenosine analogues such as uridine and cytidine do not interfere. The method was used to quantify adenosine in serum samples at concentrations as low as 10 pM. Graphical abstractSchematic representation of an effective colorimetric method for adenosine detection based on target adenosine-induced side-by-side self-assembly of gold nanorods (Au NRs).

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%.

Nucleic acid functionalized fiber optic probes for sensing in evanescent wave: optimization and application

Nucleic acid functionalized evanescent wave fiber optic (EWFO) biosensors have attracted much attention due to their remarkable advantages in both device configuration and sensing performance. One critical technique in EWFO biosensor fabrication is its surface modification, which requires (1) minimal nonspecific adsorption and (2) high-quality DNA immobilization to guarantee satisfactory sensing performances. Focusing on these two requirements, a series of optimizations have been conducted in this work to develop reliable DNA-functionalized EWFO probes. Firstly, the surface planeness of EWFO probes were found to be greatly improved by a novel HF/HNO₃ mixture etching solution. Both atomic force microscopy (AFM) and X-ray photoelectron spectroscopy (XPS) were conducted to investigate the morphological structures and surface chemical compositions. Besides, EWFO sensing performances adopting moderate immobilization of irrelevant DNA were investigated for optimization purposes. Furthermore, a split aptamer based sandwich-type EWFO sensor was developed using adenosine (Ade) as the model target (LOD = 25 μM). To the best of our knowledge, this study is the first case to focus on the optimization of etching solution compositions in the fabrication of combination tapered fibers, which provides experimental basis for the understanding of the silica-etching mechanism using HF/HNO₃ mixture solution and may further inspire related researches.

Reliable DNA-functionalized optic probes for sensing in evanescent wave have been developed based a series of optimizations on the etching solution and immobilization chemistry.

Colorimetric adenosine aptasensor based on DNA cycling amplification and salt-induced aggregation of gold nanoparticles

An aptamer based assay is described for the colorimetric detection of adenosine. The presence of adenosine triggers the deformation of hairpin DNA oligonucleotide (HP1) containing adenosine aptamer and then hybridizes another unlabeled hairpin DNA oligonucleotide (HP2). This leads to the formation of a double strand with a blunt 3' terminal. After exonuclease III (Exo III)-assisted degradation, the guanine-rich strand (GRS) is released from HP2. Hence, the adenosine-HP1 complex is released to the solution where it can hybridize another HP2 and initiate many cycles of the digestion reaction with the assistance of Exo III. This leads to the generation of a large number of GRS strands after multiple cycles. The GRS stabilize the red AuNPs against aggregation in the presence of potassium ions. If, however, GRS forms a G-quadruplex, it loses its ability to protect gold nanoparticles (AuNPs) from salt-induced AuNP aggregation. Therefore, the color of the solution changes from red to blue which can be visually observed. This colorimetric assay has a 0.13 nM detection limit and a wide linear range that extends from 5 nM to 1 μM. Graphical abstract Schematic presentation of a colorimetric aptamer biosensor for adenosine detection based on DNA cycling amplification and salt-induced aggregation of gold nanoparticles.

Formulation of DNA chimera templates: Effects on emission behavior of silver nanoclusters and sensing

Single strand DNA (ssDNA) chimeras consisting of a silver nanoclusters-nucleating sequence (NC) and an aptamer are widely employed to synthesize functional silver nanoclusters (AgNCs) for sensing purpose. Despite its simplicity, this chimeric-templated AgNCs often leads to undesirable turn-off effect, which may suffer from false positive signals caused by interference. In our effort to elucidate how the relative position of NC and aptamer affects the fluorescence behavior and sensing performance, we systematically formulated these NC and aptamer regions at different position in a DNA chimera. Using adenosine aptamer as a model, we tested the adenosine-induced optical response of each design. We also investigated the effect of linker region connecting NC and aptamer, as well as different NC sequence on the sensing performance. We concluded that locating NC sequence at 5'-end exhibited the best response, with immediate fluorescence enhancement observed over a wide linear range (1-2500 μM). Our experimental findings help to explain the emission behavior and sensing performance of chimeric conjugates of AgNCs, providing an important means to formulate a better aptasensor.

Equipment-Free Quantitative Aptamer-Based Colorimetric Assay Based on Target-Mediated Viscosity Change

In this paper, we describe an aptamer-based colorimetric assay (ABCA), which integrates enzyme-loaded microparticles for signal amplification with distance measurement for equipment-free quantitative readout. The distance measurement readout is on the basis of target-induced selective reduction in viscosity of reaction solution. Its utility is well demonstrated with inexpensive, sensitive, and selective detection of adenosine (model analyte) in buffer samples and real samples of human serum and urine with the naked eye. This ABCA method just requires operators to simply count the number of colored distance-relevant marked bars on the calibrated glass microsyringes (testing containers) to provide quantitative results. It thus holds great promise for wide applications particularly in limited-resource settings.

Quantifying the Degree of Aggregation from Fluorescent Dye-Conjugated DNA Probe by Single Molecule Photobleaching Technology for the Ultrasensitive Detection of Adenosine

In this work, we demonstrated a single molecule photobleaching-based strategy for the ultrasensitive detection of adenosine. A modified split aptamer was designed to specifically recognize individual adenosine molecules in solution. The specific binding of dye-labeled short strand DNA probes onto the elongated aptamer strand in the presence of adenosine resulted in a concentration-dependent self-aggregation process. The degree-of-aggregation (DOA) of the short DNA probes on the elongated aptamer strand could then be accurately determined based on the single molecule photobleaching measurement. Through statistically analyzing the DOA under different target concentrations, a well-defined curvilinear relationship between the DOA and target molecule concentration (e.g., adenosine) was established. The limit-of-detection (LOD) is down to 44.5 pM, which is lower than those recently reported results with fluorescence-based analysis. Owing to the high sensitivity and excellent selectivity, the sensing strategy described herein would find broad applications in biomolecule analysis under complicated surroundings.

Splitting a DNAzyme enables a Na+-dependent FRET signal from the embedded aptamer

Recently, a few Na⁺-specific RNA-cleaving DNAzymes have been reported, and a Na⁺ aptamer was identified from the NaA43 and Ce13d DNAzymes. These DNAzymes and the embedded aptamer have been used for Na⁺ detection. In this work, we studied the Na⁺-dependent folding of the Ce13d DNAzyme using fluorescence resonance energy transfer (FRET). When a FRET donor and an acceptor were respectively labeled at the ends of the DNAzyme, Na⁺ failed to induce an obvious end-to-end distance change, suggesting a rigid global structure. To relax this rigidity, the Ce13d DNAzyme was systematically split at various sites on both the enzyme and the substrate strands. The Na⁺ binding activity of the split structures was characterized by 2-aminopurine fluorescence, enzymatic activity, Tb³⁺-sensitized luminescence, and DMS footprinting. Among the various constructs, the only one that retained Na⁺ binding was the split at the cleavage site, and this construct was further labeled with two dyes near the split site. This FRET result showed Na⁺-dependent folding with a K_d of 26 mM Na⁺. This study provides important structural information related to Na⁺ binding to this new aptamer, which might also be useful for future work in biosensor design.

Linear Chain Formation of Split-Aptamer Dimers on Surfaces Triggered by Adenosine

The detection of small molecules impacts various fields; however, their small size and low concentration are usually the cause of limitations in their detection. Thus, the need for biosensors with appropriate probes and signal amplification strategies is required. Aptamers are appropriate probes selected specifically against small targets such as adenosine. The possibility to split aptamers in parts led to original amplification strategies based on sandwich assays. By combining the self-assembling of oligonucleotide dimers with split-aptamer dangling ends and a surface plasmon resonance imaging technique, we developed an original amplification approach based on linear chain formation in the presence of the adenosine target. In this article, on the basis of sequence engineering, we analyzed its performance and the effect of the probe grafting density on the length of the chains formed at the surface of the biosensor.

Nano-Aptasensing in Mycotoxin Analysis: Recent Updates and Progress

Recent years have witnessed an overwhelming integration of nanomaterials in the fabrication of biosensors. Nanomaterials have been incorporated with the objective to achieve better analytical figures of merit in terms of limit of detection, linear range, assays stability, low production cost, etc. Nanomaterials can act as immobilization support, signal amplifier, mediator and artificial enzyme label in the construction of aptasensors. We aim in this work to review the recent progress in mycotoxin analysis. This review emphasizes on the function of the different nanomaterials in aptasensors architecture. We subsequently relate their features to the analytical performance of the given aptasensor towards mycotoxins monitoring. In the same context, a critically analysis and level of success for each nano-aptasensing design will be discussed. Finally, current challenges in nano-aptasensing design for mycotoxin analysis will be highlighted.

New insights into a classic aptamer: binding sites, cooperativity and more sensitive adenosine detection

The DNA aptamer for adenosine (also for AMP and ATP) is a highly conserved sequence that has recurred in a few selections. It it a widely used model aptamer for biosensor development, and its nuclear magnetic resonance structure shows that each aptamer binds two AMP molecules. In this work, each binding site was individually removed by rational sequence design, while the remaining site still retained a similar binding affinity and specificity as confirmed by isothermal titration calorimetry. The thermodynamic parameters of binding are presented, and its biochemical implications are discussed. The number of binding sites can also be increased, and up to four sites are introduced in a single DNA sequence. Finally, the different sequences are made into fluorescent biosensors based on the structure-switching signaling aptamer design. The one-site aptamer has 3.8-fold higher sensitivity at lower adenosine concentration with a limit of detection of 9.1 μM adenosine, but weaker fluorescence signal at higher adenosine concentrations, consistent with a moderate cooperativity in the original aptamer. This work has offered insights into a classic aptamer for the relationship between the number of binding sites and sensitivity, and a shorter aptamer for improved biosensor design.

Localized surface plasmon resonance-based abscisic acid biosensor using aptamer-functionalized gold nanoparticles

Abscisic acid (ABA) plays an important role in abiotic stress response and physiological signal transduction resisting to the adverse environment. Therefore, it is very essential for the quantitative detection of abscisic acid (ABA) due to its indispensable role in plant physiological activities. Herein, a new detection method based on localized surface plasmon resonance (LSPR) using aptamer-functionalized gold nanoparticles (AuNPs) is developed without using expensive instrument and antibody. In the presence of ABA, ABA specifically bind with their aptamers to form the ABA-aptamer complexes with G-quadruplex-like structure and lose the ability to stabilize AuNPs against NaCl-induced aggregation. Meanwhile, the changes of the LSPR spectra of AuNP solution occur and therefore the detection of ABA achieved. Under optimized conditions, this method showed a good linear range covering from 5×10-7 M to 5×10-5 M with a detection limit of 0.33 μM. In practice, the usage of this novel method has been demonstrated by its application to detect ABA from fresh leaves of rice with the relative error of 6.59%-7.93% compared with ELISA bioassay. The experimental results confirmed that this LSPR-based biosensor is simple, selective and sensitive for the detection of ABA. The proposed LSPR method could offer a new analytical platform for the detection of other plant hormones by changing the corresponding aptamer.

G-quadruplex based Exo III-assisted signal amplification aptasensor for the colorimetric detection of adenosine

Adenosine is an endogenous nucleotide pivotally involved in nucleic acid and energy metabolism. Its excessive existence may indicate tumorigenesis, typically lung cancer. Encouraged by its significance as the clinical biomarker, sensitive assay methods towards adenosine have been popularized, with high cost and tedious procedures as the inevitable defects. Herein, we report a label-free aptamer-based exonuclease III (Exo III) amplification colorimetric aptasensor for the highly sensitive and cost-effective detection of adenosine. The strategy employed two unlabeled hairpin DNA oligonucleotides (HP1 and HP2), where HP1 contained the aptamer towards adenosine and HP2 embedded the guanine-rich sequence (GRS). In the presence of adenosine, hairpin HP1 could form specific binding with adenosine and trigger the unfolding of HP1's hairpin structure. The resulting adenosine-HP1 complex could hybridize with HP2, generating the Exo III recognition site. After Exo III-assisted degradation, the GRS was released from HP2, and the adenosine-HP1 was released back to the solution to combine another HP2, inducing the cycling amplification. After multiple circulations, the released ample GRSs were induced to form G-quadruplex, further catalyzing the oxidation of TMB, yielding a color change which was finally mirrored in the absorbance change. On the contrary, the absence of adenosine failed to unfold HP1, remaining color unchanged eventually. Thanks to the amplification strategy, the limit of detection was lowered to 17 nM with a broad linear range from 50 nM to 6 μM. The proposed method was successfully applied to the detection of adenosine in biological samples and satisfying recoveries were acquired.

A target triggered proximity combination-based fluorescence sensing strategy for adenosine detection

Adenosine is a potent physiological and pharmacological regulator, and its abnormal level is closely related to disease development. The sensitive and specific detection of adenosine is crucial for health evaluation and disease diagnosis. In this work, a target triggered proximity combination-based fluorescence sensing strategy is developed for the sensitive and specific detection of adenosine. A difunctional probe showing target recognition and signal amplification is designed, by integration of DNA linker-connected split aptamer fragments with a fragment-elongated polymerase/nicking template. The presence of adenosine would glue the split aptamers, which triggers the two distal aptamer fragments to combine with each other into proximity. The approaching aptamer fragment ends then initiate the strand displacement amplification (SDA) reaction, generating numerous DNA primers. The DNA primers further hybridize with a padlock probe and initiate the rolling circle amplification (RCA) reaction, producing numerous G-quadruplex sequences. The G-quadruplex sequences finally bind with Thioflavin T to obtain enhanced fluorescence signals. The method exhibits a linear correlation within the adenosine concentration range from 5.0 × 10^-7 M to 2.0 × 10^-5 M (R = 0.999) with a detection limit of 8.4 × 10^-8 M, and a good selectivity to distinguish adenosine from its analogues. The recoveries of adenosine in human serum are from 91% to 94%, demonstrating that the system works well in biological fluids. The proposed sensing strategy is anticipated to hold promise in biochemical research, clinical diagnosis and disease treatment.

A colorimetric nanosensor based on a selective target-responsive aptamer kissing complex

Herein, we report a novel approach for the design of a colorimetric aptasensor based on functionalized gold nanoparticle probes. This approach relies on the conjugation of nanoparticles by two functional DNA and RNA hairpins that engage specific kissing (loop-loop) interactions in response to the addition of a small analyte ligand, leading to particle aggregation and then red-to-purple colour change of the colloidal solution.

Probing Cellular Molecules with PolyA-Based Engineered Aptamer Nanobeacon

Adenosine triphosphate (ATP) is a central metabolite that is of critical importance in many cellular processes. The development of sensitive and selective methods for the detection of ATP level in vivo is crucial in diagnostic and theranostic applications. In this work, we have developed a polyA-based aptamer nanobeacon (PAaptNB) with improved efficiency and speed of ATP analysis. We found that the dissociation constants and competitive binding kinetics of the PAaptNB could be programmably regulated by adjusting the polyA length. When the polyA length reached to 30 bases, a 10 μM detection limit for ATP assay with PAaptNB can be achieved (∼10-fold improvement compared with the conventional thiol-based aptamer nanobeacon). The feasibility of the PAaptNB for in vivo assay was further demonstrated by imaging intracellular ATP molecules. This study provides a new strategy to construct high-efficiency and high-speed biosensors for cellular molecules analysis, which holds great potential in bioanalysis and theranostic applications.

Convection-Driven Pull-Down Assays in Nanoliter Droplets Using Scaffolded Aptamers

One of the great challenges in cellular studies is to develop a rapid and biocompatible analytical tool for single-cell analysis. We report a rapid, DNA nanostructure-supported aptamer pull-down (DNaPull) assay under convective flux in a glass capillary for analyzing the contents of droplets with nano- or picoliter volumes. We have demonstrated that the scaffolded aptamer can greatly improve the efficiency of target molecules' pull down. The convective flux allows complete reaction in <5 min, which is an 18-fold improvement compared to purely diffusive flux (traditional model of the stationary case). This established DNaPull assay can serve as a rapid and sensitive analytical platform for analyzing a variety of bioactive molecules, including small molecules [ATP, limit of detecton (LOD) of 1 μM], a drug (cocaine, LOD of 1 μM), and a biomarker (thrombin, LOD of 0.1 nM). Significantly, the designed microfluidic device compartmentalizes live cells into nanoliter-sized droplets to present single-cell samples. As a proof of concept, we demonstrated that cellular molecules (ATP) from a discrete number of HNE1 cells (zero to five cells) lysed inside nanoliter-sized droplets can be analyzed using our DNaPull assay, in which the intracellular ATP level was estimated to be ∼3.4 mM. Given the rapid assay feature and single-cell sample analysis ability, we believe that our analytical platform of convection-driven DNaPull in a glass capillary can provide a new paradigm in biosensor design and will be valuable for single-cell analysis.

A nanoparticle-based thermo-dynamic aptasensor for small molecule detection

Small molecules (MW < 1000 Da) represent a large class of biomarkers of interest. Recently, a new class of biosensors has been emerging thanks to the recognition properties of aptamers, short DNA or RNA single strands, selected against such small molecular targets. Among them, an adenosine-specific aptamer has been largely described and used due to its remarkable affinity to this small target (K_D = 6 μM). In this paper, we achieved the proof-of-principle of an aptasensor based on the thermodynamic follow-up of adenosine binding with engineered split-aptamer sequences. The detection is carried out by surface plasmon resonance imaging of split-aptamer micro-arrays, while signal amplification is ensured by gold nanoparticles (AuNPs). This original approach based on DNA sequence engineering and AuNP conjugation enabled us to reach limits of detection (LOD) 200 times lower than the K_D measured in solution with the native aptamer (LOD = 30 nM).

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.

Molecularly Imprinted Polymers with DNA Aptamer Fragments as Macromonomers

Molecularly imprinted polymers (MIPs) are produced in the presence of a template molecule. After removing the template, the cavity can selectively rebind the template. MIPs are attractive functional materials with a low cost and high stability, but traditional MIPs often suffer from low binding affinity. This study employs DNA aptamer fragments as macromonomers to improve MIPs. The DNA aptamer for adenosine was first split into two halves, fluorescently labeled, and copolymerized into MIPs. With a fluorescence quenching assay, the importance of imprinting was confirmed. Further studies were carried out using isothermal titration calorimetry (ITC). Compared to the mixture of the free aptamer fragments, their MIPs doubled the binding affinity. Each free aptamer fragment alone cannot bind adenosine, whereas MIPs containing each fragment are effective binders. We further shortened one of the aptamer fragments, and the DNA length was pushed to as short as six nucleotides, yielding MIPs with a dissociation constant of 27 μM adenosine. This study provides a new method for preparing functional MIP materials by combining high-affinity biopolymer fragments with low-cost synthetic monomers, allowing higher binding affinity and providing a method for signaling binding based on DNA chemistry.