Nucleic acid aptamers improving fluorescence anisotropy and fluorescence polarization assays for small molecules

Polycations as Aptamer-Binding Modulators for Sensitive Fluorescence Anisotropy Assay of Aflatoxin B1

Fluorescence induced by the excitation of a fluorophore with plane-polarized light has a different polarization depending on the size of the fluorophore-containing reagent and the rate of its rotation. Based on this effect, many analytical systems have been implemented in which an analyte contained in a sample and labeled with a fluorophore (usually fluorescein) competes to bind to antibodies. Replacing antibodies in such assays with aptamers, low-cost and stable oligonucleotide receptors, is complicated because binding a fluorophore to them causes a less significant change in the polarization of emissions. This work proposes and characterizes the compounds of the reaction medium that improve analyte binding and reduce the mobility of the aptamer-fluorophore complex, providing a higher analytical signal and a lower detection limit. This study was conducted on aflatoxin B1 (AFB1), a ubiquitous toxicant contaminating foods of plant origins. Eight aptamers specific to AFB1 with the same binding site and different regions stabilizing their structures were compared for affinity, based on which the aptamer with 38 nucleotides in length was selected. The polymers that interact reversibly with oligonucleotides, such as poly-L-lysine and polyethylene glycol, were tested. It was found that they provide the desired reduction in the depolarization of emitted light as well as high concentrations of magnesium cations. In the selected optimal medium, AFB1 detection reached a limit of 1 ng/mL, which was 12 times lower than in the tris buffer commonly used for anti-AFB1 aptamers. The assay time was 30 min. This method is suitable for controlling almond samples according to the maximum permissible levels of their contamination by AFB1. The proposed approach could be applied to improve other aptamer-based analytical systems.

DNA Probes for Cas12a-Based Assay with Fluorescence Anisotropy Enhanced Due to Anchors and Salts

CRISPR/Cas12a is a potent biosensing tool known for its high specificity in DNA analysis. Cas12a recognizes the target DNA and acquires nuclease activity toward single-stranded DNA (ssDNA) probes. We present a straightforward and versatile approach to transforming common Cas12a-cleavable DNA probes into enhancing tools for fluorescence anisotropy (FA) measurements. Our study involved investigating 13 ssDNA probes with linear and hairpin structures, each featuring fluorescein at one end and a rotation-slowing tool (anchor) at the other. All anchors induced FA changes compared to fluorescein, ranging from 24 to 110 mr. Significant FA increases (up to 180 mr) were obtained by adding divalent metal salts (Mg2+, Ca2+, Ba2+), which influenced the rigidity and compactness of the DNA probes. The specific Cas12a-based recognition of double-stranded DNA (dsDNA) fragments of the bacterial phytopathogen Erwinia amylovora allowed us to determine the optimal set (probe structure, anchor, concentration of divalent ion) for FA-based detection. The best sensitivity was obtained using a hairpin structure with dC10 in the loop and streptavidin located near the fluorescein at the stem in the presence of 100 mM Mg2+. The detection limit of the dsDNA target was equal to 0.8 pM, which was eight times more sensitive compared to the common fluorescence-based method. The enhancing set ensured detection of single cells of E. amylovora per reaction in an analysis based on CRISPR/Cas12a with recombinase polymerase amplification. Our approach is universal and easy to implement. Combining FA with Cas12a offers enhanced sensitivity and signal reliability and could be applied to different DNA and RNA analytes.

Integrating Ligands into Nucleic Acid Systems

Signal transduction from non-nucleic acid ligands (small molecules and proteins) to structural changes of nucleic acids plays a crucial role in both biomedical analysis and cellular regulations. However, how to bridge between these two types of molecules without compromising the expandable complexity and programmability of the nucleic acid nanomachines is a critical challenge. Compared with the previously most widely applied transduction strategies, we review the latest advances of a kinetically controlled approach for ligand-oligonucleotide transduction in this Concept article. This new design works through an intrinsic conformational alteration of the nucleic acid aptamer upon the ligand binding as a governing factor for nucleic acid strand displacement reactions. The functionalities and applications of this transduction system as a ligand converter on biosensing and DNA computation are described and discussed. Furthermore, we propose some potential scenarios for utilization of this ligand transduction design to regulate gene expression through synthetic RNA switches in the cellular contexts. Finally, future perspectives regarding this ligand-oligonucleotide transduction platform are also discussed.

Advanced biosensors for mycotoxin detection incorporating miniaturized meters

Advanced biosensors, considered as emerging technologies, are capable of accurate, quantitative and real-time analysis for point-of-care testing (POCT) applications. Moreover, the integrating of miniaturized meters into these advanced biosensors makes them ideally appropriate for portable, sensitive and selective detection of biomolecules. Miniaturized meters including PGMs (personal glucose meters), thermometer, pressuremeter, pH meter, etc. are the most accurate devices and wide availability in the market, exhibiting a promising potential towards detection of small molecule mycotoxins. In this article, we introduce and analyze the recent advancements for sensing of mycotoxins measured by handheld meters since the first report in 2012. Furthermore, limitations and challenges for versatile meters application against mycotoxins in food matrix are highlighted. By overcoming the bottleneck problems, we believe the miniaturized meters-based biosensor platform will provide great possibilities for mycotoxins analysis and launch them to the market.

An adhesive SERS substrate based on a stretched silver nanowire-tape for the in situ multicomponent analysis of pesticide residues

Two essential factors in powerful surface-enhanced Raman spectroscopy analysis of trace pesticide residues are viz., high sensitivity and efficient sampling. Herein, owing to elastic properties, a stretched Ag nanowire (Ag NW)-tape under the strain of 15% formed a wrinkled structure with periodic microridges and microgrooves, where abundant nanogaps were generated by the aggregated Ag NWs. Compared with the unstretched Ag NW-tape substrate, an appreciable signal enhancement of the modified 4-mercaptobenzoic acid (4-MBA) molecules with a ratio of 2.6 was discerned from the sophisticated SERS substrate due to the electromagnetic enhancement induced by the relatively high density of "hot spots" around the Ag NW aggregates. The as-fabricated Ag NW-tape substrate performed admirably in detecting 4-MBA and demonstrated an enhancement factor of 1.16 × 10⁶. Moreover, for the in situ detection of tetramethylthiuram disulfide, thiabendazole, and their mixture, the relatively high recovery rates of over 88% were favorably realized by the Ag NW-tape substrate with superior sensitivity, distinct flexibility, and adhesiveness. This fascinating SERS substrate, dependent on the flexible and adhesive Ag NW-tape, is promising for application in SERS analysis of trace residues on various practical surfaces.

A fluorescent assay for sensitive detection of kanamycin by split aptamers and DNA-based copper/silver nanoclusters

Kanamycin was a group of essential antibiotics generally served in treating infections of animals which leached into the environment residual in food, causing health concerns. Thus, selective and sensitive monitoring of kanamycin was significant for food safety. In this work, split aptamers were used as templates to prepare fluorescent Cu/Ag NCs for detection of kanamycin. According to the impressive affinity of the aptamer to kanamycin, two different detection modes were designed using kanamycin aptamer as a recognition molecule, in which one was to combine split aptamer Apt-1 with Apt-2 to form an entangled DNA as a Cu/Ag NCs template, the other was to associate the normal aptamer after encirclement to form Cu/Ag NCs templates. After the addition of kanamycin, the fluorescence signals of the Cu/Ag NCs synthesized in the two modes were both enhanced, but the approach with split aptamer exhibited a superior observable sensitivity than that of the normal type. The detection range showed a well linear relationship between 80 nM and 10 μM when the emission wavelength was 560 nm, and the detection limit was 13.3 nM. In addition, when streptomycin, oxytetracycline, chloramphenicol and chlortetracycline were involved in the selective interference experiment under the same conditions, the fluorescence intensity of the system performed no significant changes. The results demonstrated that this method possessed favorable specificity and selectivity for the assay of kanamycin, proficiently achieving efficient, rapid and sensitive evaluation of kanamycin in the milk samples.

Self-Assembly of Multivalent Aptamer-Tethered DNA Monolayers Dedicated to a Fluorescence Polarization-Responsive Circular Isothermal Strand Displacement Amplification for Salmonella Assay

Pathogenic bacteria are pathogens widely spread that are capable of causing mild to life-threatening diseases in human beings or other organisms. Rationally organizing the simple helical motif of double-stranded DNA (dsDNA) tiles into designed ensemble structures with architecturally defined collective properties could lead to promising biosensing applications for pathogen detection. In this work, we facilely engineered multivalent hairpin aptamer probe-tethered DNA monolayers (MHAP-DNA monolayers) and applied them to build a fluorescence polarization-responsive circular isothermal strand displacement amplification (FP-CSDA) for Salmonella assay. In this system, the MHAP-DNA monolayers were constructed based on a dsDNA tile-directed self-assembly. A FAM-labeled reporting probe (RP^FAM) with an inherent low FP signal serves as the signaling unit. The presence of target Salmonella leads to the trapping of F RP^FAM into the super DNA monolayers via a target-triggered CSDA to peel off the tethered hairpin-structured aptamer probes (HAPs) responsible for the binding of RP^FAM. As a result, the FP signal of the FAM fluorophore can be remarkably amplified due to the recycling of target Salmonella and the capacity of structural DNA materials to strongly restrict the free rotation of the FAM fluorophore but without a fluorescence quenching effect. Experimental results demonstrate that the FP assay is able to detect Salmonella with a low limit of detection (LOD) of 7.2 × 10⁰ CFU/mL and high specificity. As a proof-of-concept study, we envision our study using DNA nanoarchitecture as the foundation to modulate CSDA-based FP assays, promising to open up a new avenue for disease diagnosis, food safety detection, and biochemical studies.

Recent Developments in G-Quadruplex Binding Ligands and Specific Beacons on Smart Fluorescent Sensor for Targeting Metal Ions and Biological Analytes

The G-quadruplex structure is crucial in several biological processes, including DNA replication, transcription, and genomic maintenance. G-quadruplex-based fluorescent probes have recently gained popularity because of their ease of use, low cost, excellent selectivity, and sensitivity. This review summarizes the latest applications of G-quadruplex structures as detectors of genome-wide, enantioselective catalysts, disease therapeutics, promising drug targets, and smart fluorescence probes. In every section, sensing of G-quadruplex and employing G4 for the detection of other analytes were introduced, respectively. Since the discovery of the G-quadruplex structure, several studies have been conducted to investigate its conformations, biological potential, stability, reactivity, selectivity for chemical modification, and optical properties. The formation mechanism and advancements for detecting different metal ions (Na⁺, K⁺, Ag⁺, Tl⁺, Cu⁺/Cu²⁺, Hg²⁺, and Pb²⁺) and biomolecules (AMP, ATP, DNA/RNA, microRNA, thrombin, T4 PNK, RNase H, ALP, CEA, lipocalin 1, and UDG) using fluorescent sensors based on G-quadruplex modification, such as dye labels, artificial nucleobase moieties, dye complexes, intercalating dyes, and bioconjugated nanomaterials (AgNCs, GO, QDs, CDs, and MOF) is described herein. To investigate these extremely efficient responsive agents for diagnostic and therapeutic applications in medicine, fluorescence sensors based on G-quadruplexes have also been employed as a quantitative visualization technique.

A Sensitive Aptamer Fluorescence Anisotropy Sensor for Cd2+ Using Affinity-Enhanced Aptamers with Phosphorothioate Modification

Rapid and sensitive detection of heavy metal cadmium ions (Cd²⁺) is of great significance to food safety and environmental monitoring, as Cd²⁺ contamination and exposure cause serious health risk. In this study we demonstrated an aptamer-based fluorescence anisotropy (FA) sensor for Cd²⁺ with a single tetramethylrhodamine (TMR)-labeled 15-mer Cd²⁺ binding aptamer (CBA15), integrating the strengths of aptamers as affinity recognition elements for preparation, stability, and modification, and the advantages of FA for signaling in terms of sensitivity, simplicity, reproducibility, and high throughput. In this sensor, the Cd²⁺-binding-induced aptamer structure change provoked significant alteration of FA responses. To acquire better sensing performance, we further introduced single phosphorothioate (PS) modification of CBA15 at a specific phosphate backbone position, to enhance aptamer affinity by possible strong interaction between sulfur and Cd²⁺. The aptamer with PS modification at the third guanine (G) nucleotide (CBA15-G3S) had four times higher affinity than CBA15. Using as an aptamer probe CBA15-G3S with a TMR label at the 12th T, we achieved sensitive selective FA detection of Cd²⁺, with a detection limit of 6.1 nM Cd²⁺. This aptamer-based FA sensor works in a direct format for detection without need for labeling Cd²⁺, overcoming the limitations of traditional competitive immuno-FA assay using antibodies and fluorescently labeled Cd²⁺. This FA method enabled the detection of Cd²⁺ in real water samples, showing broad application potential.

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

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

Nucleic Acids as Biotools at the Interface between Chemistry and Nanomedicine in the COVID-19 Era

The recent development of mRNA vaccines against the SARS-CoV-2 infection has turned the spotlight on the potential of nucleic acids as innovative prophylactic agents and as diagnostic and therapeutic tools. Until now, their use has been severely limited by their reduced half-life in the biological environment and the difficulties related to their transport to target cells. These limiting aspects can now be overcome by resorting to chemical modifications in the drug and using appropriate nanocarriers, respectively. Oligonucleotides can interact with complementary sequences of nucleic acid targets, forming stable complexes and determining their loss of function. An alternative strategy uses nucleic acid aptamers that, like the antibodies, bind to specific proteins to modulate their activity. In this review, the authors will examine the recent literature on nucleic acids-based strategies in the COVID-19 era, focusing the attention on their applications for the prophylaxis of COVID-19, but also on antisense- and aptamer-based strategies directed to the diagnosis and therapy of the coronavirus pandemic.

An amplified fluorescence polarization assay for sensitive sensing of organophosphorus pesticides via MnO2 nanosheets

It is highly desirable to develop a simple, efficient and sensitive strategy for organophosphorus pesticides (OPs) in both environment pollution and human health. Herein, a novel amplified fluorescence polarization (FP) biosensor was established for highly sensitive detection of OPs using MnO₂ nanosheets as the signal enhancer. In this system, OPs can suppress the activity of acetylcholinesterase (AChE) efficiently, blocking the hydrolysis reaction of acetylthiocholine (ATCh) to generate thiocholine (TCh) by AChE. TCh can lead the decomposition of MnO₂ nanosheets to manganese ions. So, without the influence of TCh, MnO₂ nanosheets can maintain its original shape and form a stable complex with FAM-DNA, which greatly enhanced the FP signal. This method can tremendously improve the sensitivity of FP with a detection limit of 0.01 ng/mL for diazinon. In addition, it was also applicable to determine other four OPs and investigate the level of diazinon in real water samples. Consequently, the proposed approach provides a new promising platform for detection of OPs and is expected to be used in application of environmental monitoring.

Aptamer fluorescence anisotropy assays for detection of aflatoxin B1 and adenosine triphosphate using antibody to amplify signal change

Fluorescence polarization/anisotropy (FP/FA) is an attractive technology for determining small molecules in homogeneous solution based on rotation changes of a fluorescent reporter. Binding induced conformation change is a specific property of aptamers. This property has been integrated into aptamer based FA assays for small molecules. In this work, we reported aptamer FA assays for aflatoxin B1 (AFB1) and adenosine triphosphate (ATP) by using antibody conjugated complementary DNA at the 3′ end and a fluorescein (FAM)-labeled aptamer at the 5′ end. The hybridization of aptamer and cDNA induced a FAM label close to the large-sized antibody, which restricts the local rotation of FAM and gives high FA signal. With the addition of target, the aptamer probe binds with the target, and the aptamer–cDNA duplex is inhibited, causing FA signal decreases. This method achieved detection of 25 pM AFB1 and 1 μM ATP, respectively. The assay is promising for application.

Aptamer fluorescence anisotropy assays for small molecules (aflatoxin B1 and ATP) using antibody to amplify signal change.

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.

Advances in the Functional Nucleic Acid Biosensors for Detection of Lead Ions

Lead ions (Pb²⁺) are destructive to the natural environment and public health, so the efficient detection of Pb²⁺ is particularly important. Although the instrumental analysis methods have high accuracy, they require high cost and precise operation, which limits their wide application. Therefore, many strategies have been extensively studied for detecting Pb²⁺ by biosensors. Functional nucleic acids have become an efficient tool in this field. This review focuses on the recent biosensors of detecting Pb²⁺ based on functional nucleic acids from 2010 to 2020, in which DNAzyme, DNA G-quadruplex and aptamer will be introduced. The biosensors are divided into three categories that colorimetric, fluorometric and electrochemical biosensors according to the different reported signals. The action mechanism and detection effect of each biosensor are explained. Finally, the present situation of nucleic acid biosensor for the detection of Pb²⁺ is summarized and the future research direction is prospected.

Nucleic Acid Tests for Clinical Translation

Nucleic acids, including deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), are natural biopolymers composed of nucleotides that store, transmit, and express genetic information. Overexpressed or underexpressed as well as mutated nucleic acids have been implicated in many diseases. Therefore, nucleic acid tests (NATs) are extremely important. Inspired by intracellular DNA replication and RNA transcription, in vitro NATs have been extensively developed to improve the detection specificity, sensitivity, and simplicity. The principles of NATs can be in general classified into three categories: nucleic acid hybridization, thermal-cycle or isothermal amplification, and signal amplification. Driven by pressing needs in clinical diagnosis and prevention of infectious diseases, NATs have evolved to be a rapidly advancing field. During the past ten years, an explosive increase of research interest in both basic research and clinical translation has been witnessed. In this review, we aim to provide comprehensive coverage of the progress to analyze nucleic acids, use nucleic acids as recognition probes, construct detection devices based on nucleic acids, and utilize nucleic acids in clinical diagnosis and other important fields. We also discuss the new frontiers in the field and the challenges to be addressed.

Aptamer Switches Regulated by Post-Transition/Transition Metal Ions

We introduced an aptamer switch design that relies on the ability of post-transition/transition metal ions to trigger, through their coordination to nucleobases, substantial DNA destabilization. In the absence of molecular target, the addition of one such metal ion to usual aptamer working solutions promotes the formation of an alternative, inert DNA state. Upon exposure to the cognate compound, the equilibrium is shifted towards the competent DNA form. The switching process was preferentially activated by metal ions of intermediate base over phosphate complexation preference (i.e. Pb²⁺ , Cd²⁺ ) and operated with diversely structured DNA molecules. This very simple aptamer switch scheme was applied to the detection of small organics using the fluorescence anisotropy readout mode. We envision that the approach could be adapted to a variety of signalling methods that report on changes in the surface charge density of DNA receptors.

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.

Antibody- and aptamer-based competitive fluorescence polarization/anisotropy assays for ochratoxin A with tetramethylrhodamine-labeled ochratoxin A

Ochratoxin A (OTA) is one of the mycotoxins that often contaminate a variety of food stuffs, and it is a potential carcinogen for humans. Taking advantage of selective affinity binding and simple, rapid, and sensitive fluorescence polarization (FP)/fluorescence anisotropy (FA) analysis, here, we report two competitive FP/FA assays for OTA using tetramethylrhodamine (TMR)-labeled OTA as a fluorescence tracer and either antibody or aptamer as an affinity ligand to recognize OTA. In the absence of OTA, the TMR-labeled OTA binds with a large-sized affinity ligand, showing a high FA value due to the slow rotation of the affinity complex. When OTA is present, OTA competes with the TMR-labeled OTA tracer in binding limited amount of affinity ligand, causing more free TMR-labeled OTA and a significant FA decrease. We found that the antibody showed a stronger affinity towards TMR-labeled OTA compared to the aptamer. The antibody-based FA assay showed higher signal changes than the aptamer based FA assay due to the larger size of antibody over aptamer. The antibody-based competitive FA assay enabled the detection of 2.4 nM OTA, while the aptamer-based FA assay also achieved a detection limit of 2.4 nM OTA at 10 °C with the help of streptavidin conjugation to increase the molecular size and to improve aptamer affinity. These two competitive FA assays were selective, showing capability for analysis in diluted red wine.

Fluorescence Polarization-Based Bioassays: New Horizons

Fluorescence polarization holds considerable promise for bioanalytical systems because it allows the detection of selective interactions in real time and a choice of fluorophores, the detection of which the biosample matrix does not influence; thus, their choice simplifies and accelerates the preparation of samples. For decades, these possibilities were successfully applied in fluorescence polarization immunoassays based on differences in the polarization of fluorophore emissions excited by plane-polarized light, whether in a free state or as part of an immune complex. However, the results of recent studies demonstrate the efficacy of fluorescence polarization as a detected signal in many bioanalytical methods. This review summarizes and comparatively characterizes these developments. It considers the integration of fluorescence polarization with the use of alternative receptor molecules and various fluorophores; different schemes for the formation of detectable complexes and the amplification of the signals generated by them. New techniques for the detection of metal ions, nucleic acids, and enzymatic reactions based on fluorescence polarization are also considered.

Advances in the Application of Aptamer Biosensors to the Detection of Aminoglycoside Antibiotics

Antibiotic abuse is becoming increasingly serious and the potential for harm to human health and the environment has aroused widespread social concern. Aminoglycoside antibiotics (AGs) are broad-spectrum antibiotics that have been widely used in clinical and animal medicine. Consequently, their residues are commonly found in animal-derived food items and the environment. A simple, rapid, and sensitive detection method for on-site screening and detection of AGs is urgently required. In recent years, with the development of molecular detection technology, nucleic acid aptamers have been successfully used as recognition molecules for the identification and detection of AGs in food and the environment. These aptamers have high affinities, selectivities, and specificities, are inexpensive, and can be produced with small batch-to-batch differences. This paper reviews the applications of aptamers for AG detection in colorimetric, fluorescent, chemiluminescent, surface plasmon resonance, and electrochemical sensors for the analysis in food and environmental samples. This study provides useful references for future research.

A simple fluorescence anisotropy assay for detection of bisphenol A using fluorescently labeled aptamer

Bisphenol A (BPA) is one of the environmental endocrine disruptors (EDCs), and BPA contamination in environment can cause high risks to human health. Rapid determination of BPA on sites is in high demand in environmental analysis. Taking advantage of aptamers as affinity ligands and fluorescence anisotropy (FA) analysis, we developed a simple and rapid FA assay for BPA by employing a single tetramethylrhodamine (TMR) labeled short 35-mer DNA aptamer against BPA. The assay is based on the BPA-binding induced conformation change of TMR-labeled aptamer and alteration of interaction between TMR and guanine bases, resulting in change of FA signals. We screened the FA change of aptamer probes having TMR label on a specific site of the aptamer upon BPA addition. The aptamer with a TMR label on the 22nd T base showed large FA-decreasing response to BPA and maintained good binding affinity to BPA. By using this TMR-labeled aptamer, we achieved FA detection of BPA with a detection limit of 0.5 μmol/L under the optimized conditions. This assay was selective towards BPA and enabled the detection of BPA spiked in tap water sample, showing the potential applications on water samples.

Fluorescence-based quantitative platform for ultrasensitive food allergen detection: From immunoassays to DNA sensors

Food allergies are global health issue with an increasing prevalence that affect food safety; hence, food allergen detection, labeling, and management are considered to be important priorities in the food industry. In this critical review, we provide a comprehensive overview of several fluorescence-based platforms based on different biorecognition ligands, such as antibodies, DNA, aptamers, and cells, for food allergen quantification. Traditional analytical methods are generally unsuitable for food manufacturers to accomplish the real-time identification of food allergens in food products. Therefore, it is important to develop simple, rapid, inexpensive, accurate, and sensitive methods to improve user accessibility. A fluorescence-based quantitative platform provides an excellent detection platform for food allergens because of its high sensitivity. This review summarizes the traditional antibody-based fluorescent techniques for food allergen detection, such as the time-resolved fluoroimmunoassay , immunofluorescence imaging, fluorescence enzyme-linked immune sorbent assay, flow injection fluoroimmunoassay, and fluorescence immunosensors. However, these methods suffer from disadvantages such as the significant rate of false-positive and false-negative results due to antibody cross-reactivity with nontarget food components in the complex food matrix and epitope degradation during food processing. Hence, different types of fluorescence-based immunoassays are suitable for standardization and quantification of allergens in fresh foods. In addition, we summarize new fluorescence-based quantitative platforms, including fluorescence genosensors, fluorescence cell sensors, and fluorescence aptamer sensors. With the advantages of high sensitivity and simple operation, fluorescence biosensors will have great potential in the future and could provide portable methods for multiallergen real-time detection in complex food systems.

A near-infrared-II fluorescence anisotropy strategy for separation-free detection of adenosine triphosphate in complex media

Fluorescence anisotropy (FA) has been widely applied for detecting and monitoring special targets in life sciences. However, matrix autofluorescence restricted its further application in complex biological samples. Herein, we report a near-infrared-II (NIR-II) FA strategy for detecting adenosine triphosphate (ATP) in human serum samples and breast cancer cell lysate, which employed NIR-II fluorescent Ag₂Se quantum dots (QDs) as tags to reduce matrix autofluorescence effect and applied graphene oxide (GO) to enhance fluorescence anisotropy signals. In the presence of ATP, the recognition between NIR-II Ag₂Se QDs labeled aptamer (QD-pDNA) and ATP led to the release of QD-pDNA from GO, resulting in the obvious decrease of FA values. ATP could be quantitatively detected in concentrations ranged from 3 nM to 2500 nM, with a detection limit down to 1.01 nM. This study showed that the developed NIR-II FA strategy could be applied for detecting targets in complex biological samples and had great potential for monitoring interactions between biomolecules in biomedical research.

Luminescent Polymorphic Co-crystals: A Promising Way to the Diversity of Molecular Assembly, Fluorescence Polarization, and Optical Waveguide

The design of molecular optoelectronic materials based on fabricating polymorphs and/or co-crystals has received much recent attention in the fields of luminescence, sensors, nonlinear optics, and so on. If the advantages of the two crystal engineering strategies above were combined, the diversity of self-assembly fashions and the tuning of photofunctional performances would be largely extended. However, such multicomponent examples have still been very limited to date. Herein, we report the construction of luminescent polymorphic co-crystals by assembly of tris(pentafluorophenyl)borane (TPFB) with 9,10-dicyanoanthracene (DCA) and acridine (AC) as paradigms. Different stacking modes and arrangement styles based on identical building block units in polymorphic co-crystals result in adjustable crystalline morphologies and variant photophysical properties (such as fluorescence wavelength, lifetimes, and up-conversion luminescence). The optimized photoluminescence quantum yield (63.1%) and lifetime (57.1 ns) are much higher than those of the pristine assembled units. In addition, two polymorphic co-crystals (DCA@TPFB-1 and AC@TPFB-2) present prominent fluorescence polarization and optical waveguide behaviors due to the highly regulated molecular orientation. Their high one-dimensional luminescence anisotropy (0.652) and low optical waveguide loss (0.0079 dB/μm) outperform most state-of-the-art low-dimensional molecular systems and thus endow them with great opportunities for photonic materials and devices. Therefore, this work not only confirms that constructing polymorphic co-crystals can be an effective way to design new photofunctional materials for luminescence and photonic applications but also discloses a deep understanding on the relationship between variant self-assembled fashions and tunable photofunctional properties of new TPFB-based molecular materials.

Functional nucleic acid-based fluorescence polarization/anisotropy biosensors for detection of biomarkers

The sensitive and selective detection of biomarkers plays a crucial role in disease diagnostics, drug discovery, and early screening of cancers. The achievement of this goal highly depends on the continuous development of biosensing technologies. Among them, fluorescence anisotropy/polarization (FA/FP) analysis receives increasing interest due to the advantage of simple operation, fast response, and no background interference. In recent decades, great progress has been achieved in FA/FP sensors thanks to the development of functional nucleic acids (FNAs) including aptamers and nucleic acid enzymes. This review focuses on FNA-based FA/FP sensors for the quantitative detection of biomarkers, such as nucleic acid, small molecules, and proteins. The design strategies, recognition elements, and practical applications are fully highlighted. The article also discusses the challenges of applying FNA-based FA/FP sensors in the next generation and the potential solutions along with future prospects. Graphical abstract.

Aptamer-Based Biosensors for Environmental Monitoring

Due to their relative synthetic and chemical simplicity compared to antibodies, aptamers afford enhanced stability and functionality for the detection of environmental contaminants and for use in environmental monitoring. Furthermore, nucleic acid aptamers can be selected for toxic targets which may prove difficult for antibody development. Of particular relevance, aptamers have been selected and used to develop biosensors for environmental contaminants such as heavy metals, small-molecule agricultural toxins, and water-borne bacterial pathogens. This review will focus on recent aptamer-based developments for the detection of diverse environmental contaminants. Within this domain, aptamers have been combined with other technologies to develop biosensors with various signal outputs. The goal of much of this work is to develop cost-effective, user-friendly detection methods that can complement or replace traditional environmental monitoring strategies. This review will highlight recent examples in this area. Additionally, with innovative developments such as wearable devices, sentinel materials, and lab-on-a-chip designs, there exists significant potential for the development of multifunctional aptamer-based biosensors for environmental monitoring. Examples of these technologies will also be highlighted. Finally, a critical perspective on the field, and thoughts on future research directions will be offered.

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.

Ultrasensitive detection of Staphylococcal enterotoxin B in milk based on target-triggered assembly of the flower like nucleic acid nanostructure

A rapid and ultrasensitive method is described for the detection of Staphylococcal enterotoxin B (SEB). It is based on the formation of the flower like nucleic acid nanostructure by integrating (a) target-induced triggering of DNA release with (b) signal amplification by a hybridization chain reaction (HCR). Firstly, partially complementary pairing of aptamer and trigger DNA forms a duplex structure. The capture DNA (cpDNA) is then placed on the surface of gold electrode through gold-thiol chemistry. In the presence of SEB, the aptamer-target conjugate is compelled to form. This causes the release of trigger DNA owing to a strong competition between aptamer and SEB. Then, the trigger DNA is subsequently hybridized with the partial complementary sequences of the cpDNA to trigger HCR with three auxiliary DNA sequences (referred to as MB1, MB2, MB3). Finally, the flower like nucleic acid nanostructures are formed and allow numerous hexaammineruthenium(iii) chloride ([Ru(NH₃)₆]³⁺, RuHex) to be absorbed on the DNA by electrostatic interaction, and thus amplify electrochemical signal. Under optimal conditions, the chronocoulometry charge difference increases linearly with the logarithm of the SEB concentrations in the range from 5 pg mL⁻¹ to 100 ng mL⁻¹ with a detection limit as low as 3 pg mL⁻¹ (S/N = 3).

A rapid and ultrasensitive method is described for the detection of Staphylococcal enterotoxin B (SEB).