Fluorescence polarization biosensor based on an aptamer enzymatic cleavage protection strategy

Biomacromolecule-Assisted Screening for Reaction Discovery and Catalyst Optimization

Reaction discovery and catalyst screening lie at the heart of synthetic organic chemistry. While there are efforts at de novo catalyst design using computation/artificial intelligence, at its core, synthetic chemistry is an experimental science. This review overviews biomacromolecule-assisted screening methods and the follow-on elaboration of chemistry so discovered. All three types of biomacromolecules discussed─enzymes, antibodies, and nucleic acids─have been used as "sensors" to provide a readout on product chirality exploiting their native chirality. Enzymatic sensing methods yield both UV-spectrophotometric and visible, colorimetric readouts. Antibody sensors provide direct fluorescent readout upon analyte binding in some cases or provide for cat-ELISA (Enzyme-Linked ImmunoSorbent Assay)-type readouts. DNA biomacromolecule-assisted screening allows for templation to facilitate reaction discovery, driving bimolecular reactions into a pseudo-unimolecular format. In addition, the ability to use DNA-encoded libraries permits the barcoding of reactants. All three types of biomacromolecule-based screens afford high sensitivity and selectivity. Among the chemical transformations discovered by enzymatic screening methods are the first Ni(0)-mediated asymmetric allylic amination and a new thiocyanopalladation/carbocyclization transformation in which both C-SCN and C-C bonds are fashioned sequentially. Cat-ELISA screening has identified new classes of sydnone-alkyne cycloadditions, and DNA-encoded screening has been exploited to uncover interesting oxidative Pd-mediated amido-alkyne/alkene coupling reactions.

Recent advances in fluorescence anisotropy/polarization signal amplification

Fluorescence anisotropy/polarization is an attractive and versatile technique based on molecular rotation in biochemical/biophysical systems. Traditional fluorescence anisotropy/polarization assays showed relatively low sensitivity for molecule detection, because widespread molecular masses are too small to produce detectable changes in fluorescence anisotropy/polarization value. In this review, we discuss in detail how the potential of fluorescence anisotropy/polarization signal approach considerably expanded through the implementation of mass amplification, recycle the target amplification, fluorescence probes structure-switching amplification, resonance energy transfer amplification, and provide perspectives at future directions and applications.

Anti-pesticide DNA aptamers fail to recognize their targets with asserted micromolar dissociation constants

Herein, we originally aimed at developing fluorescence anisotropy biosensor platforms devoted to the homogeneous-phase detection of isocarbophos and phorate pesticides by using previously isolated DNA aptamers. To achieve this, two reporting approaches displaying very high generalizability features were implemented, based on either the complementary strand or the SYBR green intercalator displacement strategies. Unfortunately, none of the transduction methods led to phorate-dependent signals. Only the SYBR green displacement method provided a small output in the presence of isocarbophos, but at an analyte concentration greater than 100 μM. In order to identify the origin of such data, isothermal titration calorimetry (ITC) experiments were subsequently performed. It was shown that aptamers bind neither isocarbophos nor phorate in free solution with the claimed micromolar dissociation constants. This work puts forward some doubts about the previously described aptasensors that rely on the use of these functional DNA molecules. It also highlights the need to carefully investigate the binding capabilities of aptamers after their isolation and to include appropriate control experiments with scrambled or mutated oligonucleotides.

Aptamer binding assays and molecular interaction studies using fluorescence anisotropy - A review

Binding of nucleic acid aptamers to specific targets and detection with fluorescence anisotropy (FA) or fluorescence polarization (FP) take advantage of the complementary features of aptamers and the fluorescence techniques. We review recent advances in affinity binding assays using aptamers and FA/FP, with an emphasis on studies of molecular interactions and identification of binding sites. Aptamers provide several benefits, including the ease of labelling fluorophores on specific sites, binding-induced changes in aptamer structures, hybridization of the aptamers to complementary sequences, changes in molecular volume upon binding of the aptamer to its target, and adsorption of aptamers onto nanomaterials. Some of these benefits have been utilized for FA/FP assays. Once the aptamer binds to its target, the resulting changes in molecular volume (size), structure, local rotation of the fluorophore, and/or the fluorescence lifetime influence changes to the FA/FP values. Measurements of these fluorescence anisotropy/polarization changes have provided insights into the molecular interactions, such as the binding affinity and the site of binding. Studies of molecular interactions conducted in homogeneous solutions, as well as those with separations, e.g., capillary electrophoresis, have been summarized in this review. Studies on mapping the position of binding in aptamers at the single nucleotide level have demonstrated a unique benefit of the FA/FP techniques and pointed to an exciting direction for future research.

Fluorescence Anisotropy-Based Signal-Off and Signal-On Aptamer Assays Using Lissamine Rhodamine B as a Label for Ochratoxin A

Ochratoxin A (OTA), a common mycotoxin, has attracted great concern as many foodstuffs can suffer from OTA contamination; OTA causes harmful effects on human and animals. Rapid and sensitive detection of OTA is demanded in many fields for agricultural product quality, food safety, and health. Aptamer fluorescence polarization/anisotropy (FP/FA) assays integrate advantages of nucleic acid aptamers (e.g., easy preparation, high stability, and low cost) and FP/FA analysis (e.g., high sensitivity, rapidity, simplicity, and robustness). Here, we report the preparation of lissamine rhodamine B labeled OTA and developed competitive aptamer fluorescence anisotropy (FA) assays for OTA with signal-off or signal-on responses by using this fluorescently labeled probe. In the signal-off FA assay, the binding between the fluorescent probe and aptamer gave a large FA signal due to molecular volume increase, and the fluorescent probe was displaced from the aptamer in the presence of OTA target, causing FA to decrease. To further enhance the FA change in the signal-off assay, large-sized streptavidin was conjugated on the aptamer, and this assay allowed for a detection limit of 2.5 nM and a more remarkable FA decrease. Furthermore, we found that the fluorescent probe could interact with Tween 20, which caused the fluorescent probe to show a higher FA value than that of the aptamer-fluorescent probe complex. A signal-on FA assay was achieved in the binding buffer containing 0.1% Tween 20, with a detection limit of 10 nM. Signal-off and signal-on FA methods both were selective and enabled detection of OTA spiked in red wine samples, showing capability for target analysis in complex sample matrix.

Panoply of Fluorescence Polarization/Anisotropy Signaling Mechanisms for Functional Nucleic Acid-Based Sensing Platforms

Fluorescence polarization/anisotropy is a very popular technique that is widely used in homogeneous-phase immunoassays for the small molecule quantification. In the present Feature, we discuss how the potential of this signaling approach considerably expanded during the last 2 decades through the implementation of a myriad of original transducing strategies that use functional nucleic acid recognition elements as a promising alternative to antibodies.

Mirror-image aptamer kissing complex for arginine-vasopressin sensing

The recently reported aptamer kissing complex (AKC) strategy has allowed for the development of a new kind of sandwich-like sensing tools. Currently AKC assays have been only applied to low molecular weight molecules and their functionality in complex matrices remains challenging. The objective of the present study broken down into two sub-aims; exploring the propensity to broaden the scope of detectable analytes and designing a more robust system for potential applications to realistic samples. An all L-configuration aptaswitch module derived from a hairpin spiegelmer specific to a larger target, i.e. the arginine-vasopressin (AVP) hormone, was elaborated. The target-induced AKC formation in presence of a specific mirror-image RNA hairpin (L-aptakiss) probe were analyzed by using fluorescence anisotropy. The mirror-image kissing complex was successfully formed when the L-AVP target bound to the engineered L-aptaswitch element. It was also established that the use of methanol as cosolvent significantly improved the assay sensitivity through the stabilization of the ternary complex. Finally, the capability of the mirror-image method to operate in 10-fold diluted, untreated human serum was illustrated. The current work revealed that the AKC concept can be expanded to a wider range of targets and converted to a L-configuration sensing platform especially suitable for bioanalysis purposes.

Label-Free Optical Biochemical Sensors via Liquid-Cladding-Induced Modulation of Waveguide Modes

We demonstrated modulation of the waveguide mode mismatch via liquid cladding of the controllable refractive index for label-free quantitative detection of concentration of chemical or biological substances. A multimode optical fiber with its core exposed was used as the sensor head with the suitable chemical modification of its surface. Injected analyte liquid itself formed the liquid cladding for the waveguide. We found that modulation of the concentration of analyte injected enables a degree of the waveguide mode mismatch to be controlled, resulting in sensitive change in optical power transmission, which was utilized for its real-time quantitative assay. We applied the device to quantitating concentration of glycerol and bovine serum albumin (BSA) solutions. We obtained experimentally the limit of detection (LOD) of glycerol concentration, 0.001% (volume ratio), corresponding to the resolvable index resolution of ∼1.02 × 10^-6 RIU (refractive index unit). The presented sensors also exhibited reasonably good reproducibility. In BSA detection, the sensor device response was sensitive to change in the refractive indices not only of liquid bulk but also of layers just above the sensing surface with higher sensitivity, providing the LOD experimentally as ∼3.7 ng/mL (mass coverage of ∼30 pg/mm²). A theoretical model was also presented to invoke both mode mismatch modulation and evanescent field absorption for understanding of the transmission change, offering a theoretical background for designing the sensor head structure for a given analyte. Interestingly, the device sensing length played little role in the important sensor characteristics such as sensitivity, unlike most of the waveguide-based sensors. This unraveled the possibility of realizing a highly simple structured label-free sensor for point-of-care testing in a real-time manner via an optical waveguide with liquid cladding. This required neither metal nor dielectric coating but still produced sensitivity comparable to those of other types of label-free sensors such as plasmonic fiber ones.

Use of anchor protein modules in fluorescence polarisation aptamer assay for ochratoxin A determination

A new strategy for sensitive fluorescence polarisation (FP) analysis is proposed which uses aptamer as the receptor and anchor protein modules as the enhancers by including the aptamers in complexes with protein modules. This approach is based on increasing the size differences of bound and unbound fluorophores. The strategy was applied in an ochratoxin A (ОТА) assay with the competitive binding of fluorophore-labelled and free OTA with aptamer-based receptors. We showed that the binding of labelled OTA with aptamer included in complexes with anchors led to higher a FP than binding with free aptamer. This allowed the aptamer concentration to be reduced, thus lowering the limit of detection by a factor of 40, down to 3.6 nM. The assay time was 15 min. To evaluate the applicability of the FP assay with aptamer-anchor complex to real samples, we conducted OTA measurements in spiked white wine. The OTA limit of detection in wine was 2.8 nM (1.1 μg/kg), and the recoveries ranged from 83% to 113%. The study shows that the proposed anchor strategy is efficient for increasing the sensitivity of FP-based aptamer assays.

Small molecule aptamer assays based on fluorescence anisotropy signal-enhancer oligonucleotides

Herein, we design novel fluorescence anisotropy (FA) aptamer sensing platforms dedicated to small molecule detection. The assay strategy relied on enhanced fluctuations of segmental motion dynamics of the aptamer tracer mediated by an unlabelled, partially complementary oligonucleotide. The signal-enhancer oligonucleotide (SEO) essentially served as a free probe fraction revealer. By targeting specific regions of the signalling functional nucleic acid, the SEO binding to the unbound aptamer triggered perturbations of both the internal DNA flexibility and the localized dye environment upon the free probe to duplex structure transition. This potentiating effect determined increased FA variations between the duplex and target bound states of the aptameric probe. FA assay responses were obtained with both pre-structured (adenosine) and unstructured (tyrosinamide) aptamers and with dyes of different photochemical properties (fluorescein and texas red). The multiplexed analysis ability was further demonstrated through the simultaneous multicolour detection of the two small targets. The FA method appears to be especially simple, sensitive and widely applicable.

Optimization of Experimental Parameters to Explore Small-Ligand/Aptamer Interactions through Use of (1) H NMR Spectroscopy and Molecular Modeling

Aptamers constitute an emerging class of molecules designed and selected to recognize any given target that ranges from small compounds to large biomolecules, and even cells. However, the underlying physicochemical principles that govern the ligand-binding process still have to be clarified. A major issue when dealing with short oligonucleotides is their intrinsic flexibility that renders their active conformation highly sensitive to experimental conditions. To overcome this problem and determine the best experimental parameters, an approach based on the design-of-experiments methodology has been developed. Here, the focus is on DNA aptamers that possess high specificity and affinity for small molecules, L-tyrosinamide, and adenosine monophosphate. Factors such as buffer, pH value, ionic strength, Mg(2+) -ion concentration, and ligand/aptamer ratio have been considered to find the optimal experimental conditions. It was then possible to gain new insight into the conformational features of the two ligands by using ligand-observed NMR spectroscopic techniques and molecular mechanics.

Enzymatic cleavage and mass amplification strategy for small molecule detection using aptamer-based fluorescence polarization biosensor

Fluorescence polarization (FP) assays incorporated with fluorophore-labeled aptamers have attracted great interest in recent years. However, detecting small molecules through the use of FP assays still remains a challenge because small-molecule binding only results in negligible changes in the molecular weight of the fluorophore-labeled aptamer. To address this issue, we herein report a fluorescence polarization (FP) aptamer assay that incorporates a novel signal amplification strategy for highly sensitive detection of small molecules. In the absence of adenosine, our model target, free FAM-labeled aptamer can be digested by nuclease, resulting in the release of FAM-labeled nucleotide segments from the dT-biotin/streptavidin complex with weak background signal. However, in the presence of target, the FAM-labeled aptamer-target complex protects the FAM-labeled aptamer from nuclease cleavage, allowing streptavidin to act as a molar mass amplifier. The resulting increase in molecular mass and FP intensity of the aptamer-target complex provides improved sensitivity for concentration measurement. The probe could detect adenosine from 0.5 μM to 1000 μM, with a detection limit of 500 nM, showing that the sensitivity of the probe is superior to aptamer-based FP approaches previously reported for adenosine. Importantly, FP could resist environmental interferences, making it useful for complex biological samples without any tedious sample pretreatments. Our results demonstrate that this dual-amplified, aptamer-based strategy can be used to design fluorescence polarization probes for rapid, sensitive, and selective measurement of small molecules in complicated biological environment.

Aptamer fluorescence anisotropy sensors for adenosine triphosphate by comprehensive screening tetramethylrhodamine labeled nucleotides

We previously reported a fluorescence anisotropy (FA) approach for small molecules using tetramethylrhodamine (TMR) labeled aptamer. It relies on target-binding induced change of intramolecular interaction between TMR and guanine (G) base. TMR-labeling sites are crucial for this approach. Only terminal ends and thymine (T) bases could be tested for TMR labeling in our previous work, possibly causing limitation in analysis of different targets with this FA strategy. Here, taking the analysis of adenosine triphosphate (ATP) as an example, we demonstrated a success of conjugating TMR on other bases of aptamer adenine (A) or cytosine (C) bases and an achievement of full mapping various labeling sites of aptamers. We successfully constructed aptamer fluorescence anisotropy (FA) sensors for adenosine triphosphate (ATP). We conjugated single TMR on adenine (A), cytosine (C), or thymine (T) bases or terminals of a 25-mer aptamer against ATP and tested FA responses of 14 TMR-labeled aptamer to ATP. The aptamers having TMR labeled on the 16th base C or 23rd base A were screened out and exhibited significant FA-decreasing or FA-increasing responses upon ATP, respectively. These two favorable TMR-labeled aptamers enabled direct FA sensing ATP with a detection limit of 1 µM and the analysis of ATP in diluted serum. The comprehensive screening various TMR labeling sites of aptamers facilitates the successful construction of FA sensors using TMR-labeled aptamers. It will expand application of TMR-G interaction based aptamer FA strategy to a variety of targets.

Capillary gel electrophoresis-coupled aptamer enzymatic cleavage protection strategy for the simultaneous detection of multiple small analytes

This novel, multi small-analyte sensing strategy is the result of combining the target-induced aptamer enzymatic protection approach with the CGE-LIF (capillary gel electrophoresis with laser-induced fluorescence) technique. The implemented assay principle is based on an analysis of the phosphodiesterase I (PDE I)-mediated size variation of a fluorescein-labeled aptamer (FApt), the enzyme catalyzing the removal of nucleotides from DNA in the 3' to 5' direction. In the absence of the target, the unfolded aptamer was enzymatically cleaved into short DNA fragments. Upon target binding, the DNA substrate was partially protected against enzymatic hydrolysis. The amount of bound aptamer remaining after the exonuclease reaction was proportional to the concentration of the target. The CGE technique, which was used to determine the separation of FApt species from DNA digested products, permitted the quantification of adenosine (A), ochratoxin A (O), and tyrosinamide (T) under the same optimized enzymatic conditions. This assay strategy was subsequently applied to the simultaneous detection of A, O, and T in a single capillary under buffered conditions using corresponding FApt probes of different lengths (23, 36, and 49 nucleotides, respectively). Additionally, the detection of these three small molecules was successfully achieved in a complex medium (diluted, heat-treated human serum) showing a good recovery. It is worth noting that the multiplexed analysis was accomplished for targets with different charge states by using aptamers possessing various structural features. This sensing platform constitutes a rationalized and reliable approach with an expanded potential for a high-throughput determination of small analytes in a single capillary.

Chemical sensing of neurotransmitters

This review focuses on the chemosensors for neurotransmitters published for the last 12 years, covering biogenic amines (dopamine, epinephrine, norepinephrine, serotonin, histamine and acetylcholine), amino acids (glutamate, aspartate, GABA, glycine and tyrosine), and adenosine.

Identification of allosteric nucleotide sites of tetramethylrhodamine-labeled aptamer for noncompetitive aptamer-based fluorescence anisotropy detection of a small molecule, ochratoxin A

Aptamer-based fluorescence anisotropy (FA) assay combines the advantages of affinity aptamers in good stability, easy generation, and facile labeling and the benefits of FA in homogeneous analysis, such as robustness, simplicity, and high reproducibility. By using a fluorophore-labeled aptamer, FA detection of a small molecule is not as easy as detection of protein because the binding of a small molecule cannot cause significant increase of molecular weight of the dye-labeled aptamer. The intramolecular interaction between labeled tetramethylrhodamine (TMR) and DNA aptamer bases dramatically affects the local rotation and FA of TMR. This intramolecular interaction can be altered by aptamer conformation change upon target binding, leading to a significant change of FA of TMR. Taking this unique feature of a TMR-labeled aptamer, we described a noncompetitive aptamer-based fluorescence anisotropy assay for detection of small molecules by using ochratoxin A (OTA) as a model. We successfully identified the specific TMR-labeling sites of aptamers with sensitive FA response to OTA from the 5'-end, 3'-end and the internal thymine (T) bases. The aptamer with a TMR labeled on the 10th T base exhibited a remarkable FA reduction response to OTA (Δr = 0.078), without requiring any proteins or nanomaterials as FA signal enhancers. This FA approach for OTA showed high sensitivity with a detection limit of 3 nM, a dynamic range from 3 nM to 3 μM, and good selectivity over the tested compounds with similar structures to OTA. The new strategy allowed the detection of OTA in diluted red wine and urine samples.

Screening interaction between ochratoxin A and aptamers by fluorescence anisotropy approach

By taking advantage of the intrinsic fluorescence of ochratoxin A (OTA), we present a fluorescence anisotropy approach for rapid analysis of the interactions between OTA and aptamers. The specific binding of OTA with a 36-mer aptamer can induce increased fluorescence anisotropy (FA) of OTA as the result of the freedom restriction of OTA and the increase of molecular volume, and the maximum FA change is about 0.160. This FA approach enables an easy way to investigate the effects of buffer compositions like metal ions on the affinity binding. FA analysis shows the interaction between OTA and aptamer is greatly enhanced by the simultaneous presence of Ca(2+) and Na(+), while the binding affinity of aptamer decreases more than 18-fold when only Ca(2+) exists, and the binding is completely lost when Ca(2+) is absent. Crucial region of the aptamer for binding can be mapped through FA analysis and aptamer mutation. The demonstrated FA approach maintains the advantages of FA in simplicity, rapidity, and robustness. This investigation will help the development of aptamer-based assays for OTA detection in optimizing the binding conditions, modification of aptamers, and rational design.

Microfluidic channel with embedded SERS 2D platform for the aptamer detection of ochratoxin A

A selective aptameric sequence is adsorbed on a two-dimensional nanostructured metallic platform optimized for surface-enhanced Raman spectroscopy (SERS) measurements. Using nanofabrication methods, a metallic nanostructure was prepared by electron-beam lithography onto a glass coverslip surface and embedded within a microfluidic channel made of polydimethylsiloxane, allowing one to monitor in situ SERS fingerprint spectra from the adsorbed molecules on the metallic nanostructures. The gold structure was designed so that its localized surface plasmon resonance matches the excitation wavelength used for the Raman measurement. This optofluidic device is then used to detect the presence of a toxin, namely ochratoxin-A (OTA), in a confined environment, using very small amounts of chemicals, and short data acquisition times, by taking advantage of the optical properties of a SERS platform to magnify the Raman signals of the aptameric monolayer system and avoiding chemical labeling of the aptamer or the OTA target.

Nucleic acid fluorescent probes for biological sensing

Nucleic acid fluorescent probes are playing increasingly important roles in biological sensing in recent years. In addition to the conventional functions of single-stranded DNA/RNA to hybridize with their complementary strands, affinity nucleic acids (aptamers) with specific target binding properties have also been developed, which has greatly broadened the application of nucleic acid fluorescent probes to the detection of a large variety of analytes, including small molecules, proteins, ions, and even whole cells. Another chemical property of nucleic acids is to act as substrates for various nucleic acid enzymes. This property can be utilized not only to detect those enzymes and screen their inhibitors, but also employed to develop effective signal amplification systems, which implies extensive applications. This review mainly covers the biosensing methods based on the above three types of nucleic acid fluorescent probes. The most widely used intensity-based biosensing assays are covered first, including nucleic acid probe-based signal amplification methods. Then fluorescence lifetime, fluorescence anisotropy, and fluorescence correlation spectroscopy assays are introduced, respectively. As a rapidly developing field, fluorescence imaging approaches are also briefly summarized.

Nucleic acid aptamers against biotoxins: a new paradigm toward the treatment and diagnostic approach

Nucleic acid aptamers are short single-stranded DNA or RNA oligonucleotides that can bind to their targets with very high affinity and specificity, and are generally selected by a process referred to as systematic evolution of ligands by exponential enrichment. Conventional antibody-based therapeutic and diagnostic approach currently employed against biotoxins pose major limitations such as the requirement of a live animal for the in vivo enrichment of the antibody species, decreased stability, high production cost, and side effects. Aptamer technology is a viable alternative that can be used to combat these problems. Fully sequestered in vitro, aptamers eliminate the need for a living host. Furthermore, one of the key advantages of using aptamers instead of antibodies is that they can be selected against very weakly immunogenic and cytotoxic substances. In this review, we focus on nucleic acid aptamers developed against various biotoxins of plant, microorganism, or animal origin and show how these can be used in diagnostics (e.g., biosensors) and therapy.

Single-stranded DNA binding protein-assisted fluorescence polarization aptamer assay for detection of small molecules

Here, we describe a new fluorescence polarization aptamer assay (FPAA) strategy which is based on the use of the single-stranded DNA binding (SSB) protein from Escherichia coli as a strong FP signal enhancer tool. This approach relied on the unique ability of the SSB protein to bind the nucleic acid aptamer in its free state but not in its target-bound folded one. Such a feature was exploited by using the antiadenosine (Ade)-DNA aptamer (Apt-A) as a model functional nucleic acid. Two fluorophores (fluorescein and Texas Red) were introduced into different sites of Apt-A to design a dozen fluorescent tracers. In the absence of the Ade target, the binding of the labeled aptamers to SSB governed a very high fluorescence anisotropy increase (in the 0.130-0.200 range) as the consequence of (i) the large global diffusion difference between the free and SSB-bound tracers and (ii) the restricted movement of the dye in the SSB-bound state. When the analyte was introduced into the reaction system, the formation of the folded tertiary structure of the Ade-Apt-A complex triggered the release of the labeled nucleic acids from the protein, leading to a strong decrease in the fluorescence anisotropy. The key factors involved in the fluorescence anisotropy change were considered through the development of a competitive displacement model, and the optimal tracer candidate was selected for the Ade assay under buffer and realistic (diluted human serum) conditions. The SSB-assisted principle was found to operate also with another aptamer system, i.e., the antiargininamide DNA aptamer, and a different biosensing configuration, i.e., the sandwich-like design, suggesting the broad usefulness of the present approach. This sensing platform allowed generation of a fluorescence anisotropy signal for aptamer probes which did not operate under the direct format and greatly improved the assay response relative to that of the most previously reported small target FPAA.