Recent progress in nanomaterial-enhanced fluorescence polarization/anisotropy sensors

A novel CRISPR-Cas12a-based fluorescence anisotropy method with a high signal-to-background ratio for sensitive biosensing

Here, a CRISPR-Cas12a system with high trans-cleavage ability integrating a DNA nanochain formed by DNA tetrahedrons with a large molecular mass was employed to enhance the signal-to-background ratio of the fluorescence anisotropy method for achieving sensitive detection of hepatitis B virus DNA.

Explore the toxicological mechanism of 6PPD-Q on human health through a novel perspective: The interaction between lactate dehydrogenase and 6PPD-Q

N-(1,3-dimethylbutyl)-N'-phenyl-p-phenylenediamine-quinone (6PPD-Q), an oxidative derivative of tire anti-degradant, has been linked to mortality in coho salmon (Oncorhynchus kisutch) and has exhibited potential human toxicity. Hence, exploring how 6PPD-Q interacts with biomacromolecules like enzymes is indispensable to assess its human toxicity and elucidate its mechanism of action. This investigation aims to explore the impact of 6PPD-Q on lactate dehydrogenase (LDH) through various methods. The findings indicate that 6PPD-Q can spontaneously embed in the coenzyme site of LDH and obviously change the biological activity of LDH by non-competitive inhibition. Simultaneously, this inhibitory effect is concentration-dependent. 6PPD-Q can affect both the level of LDH and the transcription of Ldha in AML-12 cells. Hydrogen bonding and van der Waals forces serve as the primary driving forces in LDH-6PPD-Q combination process. The apparent binding constant (Ka) value is (9.773 ± 0.699) × 103 L/mol (298 K). The presence of 6PPD-Q alters the conformation of LDH and decreases its structural stability. Moreover, the results of molecular docking indicate that the interaction of 6PPD-Q with Asp51 and Arg98 of LDH may be the reason that 6PPD-Q inhibits the biological activity of LDH. Meanwhile, the energy decomposition of residue analyses for LDH-6PPD-Q formation further highlight the energy contribution of Asp51 and Arg98 in this combination process.

Tailorable optical properties of polymer nanodots for triple-mode fluorescence detection of nucleic acids

We present a triple-mode nanosensor platform for nucleic acid detection utilizing fluorescence anisotropy and Förster resonance energy transfer (FRET) strategies. The self-assembled nanoprobes serve as mass amplifiers, nanoquenchers, or nanodonors, exhibiting high FRET efficiencies (64.4-86.5%) and demonstrating excellent detection capabilities in DNA and microRNA analysis.

Aptamer-Protein Interactions: From Regulation to Biomolecular Detection

Serving as the basis of cell life, interactions between nucleic acids and proteins play essential roles in fundamental cellular processes. Aptamers are unique single-stranded oligonucleotides generated by in vitro evolution methods, possessing the ability to interact with proteins specifically. Altering the structure of aptamers will largely modulate their interactions with proteins and further affect related cellular behaviors. Recently, with the in-depth research of aptamer-protein interactions, the analytical assays based on their interactions have been widely developed and become a powerful tool for biomolecular detection. There are some insightful reviews on aptamers applied in protein detection, while few systematic discussions are from the perspective of regulating aptamer-protein interactions. Herein, we comprehensively introduce the methods for regulating aptamer-protein interactions and elaborate on the detection techniques for analyzing aptamer-protein interactions. Additionally, this review provides a broad summary of analytical assays based on the regulation of aptamer-protein interactions for detecting biomolecules. Finally, we present our perspectives regarding the opportunities and challenges of analytical assays for biological analysis, aiming to provide guidance for disease mechanism research and drug discovery.

A Sensitive Fluorescence Polarization Immunoassay for the Rapid Detection of Okadaic Acid in Environmental Waters

In this study, a homogeneous fluorescence polarization immunoassay (FPIA) for the detection of hazardous aquatic toxin okadaic acid (OA) contaminating environmental waters was for the first time developed. A conjugate of the analyte with a fluorophore based on a fluorescein derivative (tracer) was synthesized, and its interaction with specific anti-OA monoclonal antibodies (MAbs) was tested. A MAbs-tracer pair demonstrated highly affine immune binding (KD = 0.8 nM). Under optimal conditions, the limit of OA detection in the FPIA was 0.08 ng/mL (0.1 nM), and the working range of detectable concentrations was 0.4-72.5 ng/mL (0.5-90 nM). The developed FPIA was approbated for the determination of OA in real matrices: river water and seawater samples. No matrix effect of water was observed; therefore, no sample preparation was required before analysis. Due to this factor, the entire analytical procedure took less than 10 min. Using a compact portable fluorescence polarization analyzer enables the on-site testing of water samples. The developed analysis is very fast, easy to operate, and sensitive and can be extended to the determination of other aquatic toxins or low-molecular-weight water or food contaminants.

A ratiometric fluorescent aptamer homogeneous biosensor based on hairpin structure aptamer for AFB1 detection

On the basis of aptamer (Apt) with hairpin structure and fluorescence resonance energy transfer (FRET), a ratio fluorescent aptamer homogeneous sensor was prepared for the determination of Aflatoxin B₁ (AFB1). Initially, the Apt labeled simultaneously with Cy5, BHQ2, and cDNA labeled with Cy3 were formed a double-stranded DNA through complementary base pairing. The fluorescence signal of Cy3 and Cy5 were restored and quenched respectively. Thus, the ratio change of F_Cy3 to F_Cy5 was used to realized the detection of AFB1 with wider detection range and lower limit of detection (LOD). The response of the optimized protocol for AFB1 detection was wider linear range from 0.05 ng/mL to 100 ng/mL and the LOD was 12.6 pg/mL. The sensor designed in this strategy has the advantages of simple preparation and fast signal response. It has been used for the detection of AFB1 in labeled corn and wine, and has good potential for application in real samples.

Progress in Nanomaterials-Based Enzyme and Aptamer Biosensor for the Detection of Organophosphorus Pesticides

With the improvement of people's safety awareness, the requirement of pesticide detection is gradually increasing, and many new detection methods toward Organophosphorus pesticide (OPs) has been further developed and applied. Nanomaterials-based biosensors have played an important role in the trace detection of OPs. This article mainly introduces the detection principle of enzymes and aptamers as the identification element of biosensors. Various nanomaterials (i.e., metals and metal oxides, carbon nanotubes, graphene and graphene oxide, quantum dots, metal organic frameworks, molecular imprinted polymers, etc.) possess their unique properties and play different roles in the enzyme and aptamer-based biosensors toward OPs: (a) to produce the optical or electrochemical signal; (b) as a carrier to load the enzyme or aptamer; (c) to enhance the signal response. Besides, the intelligent portable devices provide the possibility to realize the onsite and real-time detection. The limitations of some nanomaterials and the future development are discussed. Finally, the future of enzyme and aptamer-based biosensors has prospected.

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.

A turn-on fluorescent probe via substitution-rearrangement for highly sensitive and discriminative detection of cysteine and its imaging in living cells

Biothiols play an important role in many physiological and pathological processes, especially in the occurrence of oxidative stress caused by abnormal cysteine (Cys) concentration. Therefore, it is particularly critical to develop a method that can specifically identify Cys to avoid interference from other biological analytes. However, most Cys-specific fluorescent probes are difficult to distinguish between homocysteine (Hcy) and glutathione (GSH). In this work, to avoid the interference of Hcy and GSH, we developed a fluorescent probe triarylimidazole-naphthalimide-piperazine-sulfonyl benzoxadiazole (TNP-SBD-Cl) based on fluorescence resonance energy transfer (FRET) on platform of naphthalimide-sulfonyl benzoxadiazole (SBD), the main SBD 4-chlorine groups have mild reactivity to undergo substitution and rearrangement to distinguish Hcy and GSH. The TNP-SBD-Cl response to Cys would turn on FRET and generate a new yellow fluorescence with a large Stokes shift (157 nm), and with excellent selectivity and low detection limit (0.87 μM). Moreover, TNP-SBD-Cl can be used to monitor Cys in living HeLa cells with low cytotoxicity, suggesting that it has markedly diagnostic significance in physiological and pathological processes.

Enzyme-free fluorescence determination of uric acid and trace Hg(II) in serum using Si/N doped carbon dots

A new fluorescence probe method for the detection of Hg(II) in serum was established, which has the detection limit of 3.57 nM and quantification limit of 5 nM, based on the electrostatic induced agglomeration quenching and complexation between Hg(II) and silicon-nitrogen-doped carbon nanodots (Si/N-CDs). Furthermore, the fluorescence probe also showed the satisfactory results in the determination of Hg(II) in human serum. Subsequently, take advantage of the uric acid (UA) to recover the fluorescence of the Si/N-CDs-Hg(II) complex probe, another enzyme-free ways to determine UA was developed. The complex probe can selectively detect the UA content in the 0.5-30 μM range, and its detection limit can reach 0.14 μM, which has successfully detected the UA in total serum, and the results were no significant difference comparing with the controls.

Aptamer-based strategies for recognizing adenine, adenosine, ATP and related compounds

Adenine is a key nucleobase, adenosine is an endogenous regulator of the immune system, while adenosine triphosphate (ATP) is the energy source of many biological reactions. Selective detection of these molecules is useful for understanding biological processes, biochemical reactions and signaling. Since 1993, various aptamers have been reported to bind to adenine and its derivatives. In addition, the adenine riboswitch was later discovered. This review summarizes the efforts for the selection of RNA and DNA aptamers for adenine derivatives, and we pay particular attention to the specificity of binding. In addition, other molecular recognition strategies based on rational sequence design are also introduced. Most of the work in the field was performed on the classic DNA aptamer for adenosine and ATP reported by the Szostak group. Based on this aptamer, some representative applications such as the design of fluorescent, colorimetric and electrochemical biosensors, intracellular imaging, and ATP-responsive materials are also described. In addition, we critically review the limit of the reported aptamers and also important problems in the field, which can give future research opportunities.

A review on optical sensors based on layered double hydroxides nanoplatforms

In recent years, significant efforts have been devoted towards the fabrication and application of layered double hydroxides (LDHs) due to their tremendous features such as excellent biocompatibility with negligible toxicity, large surface area, high conductivity, excellent solubility, and ion exchange properties. Most impressive, LDHs offer a favorable environment to attach several substances such as quantum dots, fluorescein dyes, proteins, and enzymes, which leads to strengthening the catalytic properties or increasing the sensing selectivity and sensitivity of the resulted hybrids. With the extensive ongoing research on the application of nanomaterials, many studies have led to remarkable achievements in exploring LDHs as sensing nanoplatforms. In optical sensors, for instance, many sensing strategies were tailored based on the enzyme-mimicking properties of LDHs, including colorimetric and chemiluminescence procedures. Meanwhile, others were designed based on intercalating some fluorogenic substrates on the LDHs, whereby the sensing signal can be acquired by quenching or enhancing their fluorescence after the addition of analytes. In this review, we aim to summarize the recent advances in optical sensors that use layered double hydroxides as sensing platforms for the determination of various analytes. By outlining some representative examples, we accentuate the change of spectral absorbance, chemiluminescence, and photoluminescence phenomena triggered by the interaction of LDH or functionalized-LDH with the indicators and analytes in the system. And finally, current limitations and possible future orientation in designing further LDHs-based optical sensors are presented. It is hoped that this review will be helpful in assisting the establishment of more improved sensors based on LDHs features. Optical sensors based on layered double hydroxides (LDHs) nanoplatforms were reviewed. The sensing system and detection approaches were rationally reviewed. Possible future orientations were highlighted.

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.

Morphology-maintaining synthesis of copper hydroxy phosphate@metal-organic framework composite for extraction and determination of trace mercury in rice

A novel copper hydroxy phosphate@MOF composite DMP-Cu decorated by 2, 5-dimercapto-1, 3, 4-thiadiazol was facilely prepared and characterized. A dispersive SPE strategy using DMP-Cu as adsorbent combined with atomic fluorescence spectroscopy was developed for the selective capture of trace total mercury in rice sample. The adsorption mechanism showed that the Hg²⁺ removal process was fitted with pseudo second-order kinetics and the Langmuir adsorption model. The adsorbent was easy to be regenerated and the maximum adsorption capacity for the removal of Hg²⁺ was 249.5 mg g^-1 at the optimal pH of 4. X-ray photoelectron spectroscopy and Raman spectra verified the selective and strong interaction between Hg²⁺ and thiol/nitrogen-containing functional groups of DMTZ on DMP-Cu. The trace total mercury in rice samples was determined with detection limit of 0.0125 ng mL^-1 and relative standard deviation below 6%. The high recoveries were obtained in range of 98.8-109% for the spiked rice samples.

Zn2+ -Dependent DNAzymes: From Solution Chemistry to Analytical, Materials and Therapeutic Applications

Since 1994, deoxyribozymes or DNAzymes have been in vitro selected to catalyze various types of reactions. Metal ions play a critical role in DNAzyme catalysis, and Zn²⁺ is a very important one among them. Zn²⁺ has good biocompatibility and can be used for intracellular applications. Chemically, Zn²⁺ is a Lewis acid and it can bind to both the phosphate backbone and the nucleobases of DNA. Zn²⁺ undergoes hydrolysis even at neutral pH, and the partially hydrolyzed polynuclear complexes can affect the interactions with DNA. These features have made Zn²⁺ a unique cofactor for DNAzyme reactions. This review summarizes Zn²⁺ -dependent DNAzymes with an emphasis on RNA-/DNA-cleaving reactions. A key feature is the sharp Zn²⁺ concentration and pH-dependent activity for many of the DNAzymes. The applications of these DNAzymes as biosensors for Zn²⁺ , as therapeutic agents to cleave intracellular RNA, and as chemical biology tools to manipulate DNA are discussed. Future studies can focus on the selection of new DNAzymes with improved performance and detailed biochemical characterizations to understand the role of Zn²⁺ , which can facilitate practical applications of Zn²⁺ -dependent DNAzymes.

Thinking outside the shell: novel sensors designed from plasmon-enhanced fluorescent concentric nanoparticles

The alteration of photophysical properties of fluorophores in the vicinity of a metallic nanostructure, a phenomenon termed plasmon- or metal-enhanced fluorescence (MEF), has been investigated extensively and used in a variety of proof-of-concept demonstrations over the years. A particularly active area of development in this regard has been the design of nanostructures where fluorophore and metallic core are held in a stable geometry that imparts improved luminosity and photostability to a plethora of organic fluorophores. This minireview presents an overview of MEF-based concentric core-shell sensors developed in the past few years. These architectures expand the range of applications of nanoparticles (NPs) beyond the uses possible with fluorescent molecules. Design aspects that are being described include the influence of the nanocomposite structure on MEF, notably the dependence of fluorescence intensity and lifetime on the distance to the plasmonic core. The chemical composition of nanocomposites as a design feature is also discussed, taking as an example the use of non-noble plasmonic metals such as indium as core materials to enhance multiple fluorophores throughout the UV-Vis range and tune the sensitivity of halide-sensing fluorophores operating on the principle of collisional quenching. Finally, the paper describes how various solid substrates can be functionalized with MEF-based nanosensors to bestow them with intense and photostable pH-sensitive properties for use in fields such as medical therapy and diagnostics, dentistry, biochemistry and microfluidics.

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 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.

A novel hollow-sphere cyclodextrin nanoreactor for the enhanced removal of bisphenol A under visible irradiation

A novel hybrid nanoreactor with spatially separated co-catalysts (SH-CD-Au@CdS@MnO_x) was successfully synthesised to remove bisphenol-A (BPA) from water by visible light. The photooxidation intermediates, degradation pathway of BPA and the enhancement mechanism were investigated in particular. Gold (Au) nanoparticles modified with SH-β-cyclodextrin and MnO_x nanoparticles were selectively decorated on the interior and exterior surface of hollow CdS nanoreactors, respectively. The directed migration of photogenerated electrons and holes induced by spatially separated co-catalysts lead to high utilization of light, and SH-β-cyclodextrin modification makes catalytic active sites more accessible for oxidation intermediates. Compared with pristine CdS, the hybrid nanoreactor increased the BPA photooxidation reaction rate and the TOC removal efficiency by 5.6-fold and 3.6-fold, respectively. Moreover, the toxic intermediates, such as phenol, were further degraded by visible light. Molecular orbital calculation predicted that the sites on BPA molecule values of (FED²_HOMO + FED²_LUMO) can be easier attacked by the radical, whereas atoms with higher values of 2FED²_HOMO can easily be extracted into electrons. Thus, SH-CD-Au@CdS@MnO_x can provide a new strategy for the high-efficiency photodegradation of endocrine disrupter compounds in advanced water treatments.

Fluorescence Polarization for Probing DNA Adsorption by Nanomaterials and Fluorophore/DNA Interactions

Fluorescence polarization (FP) is attractive for measuring binding interactions and has been recently used to study DNA adsorption on nanomaterials. Since most nanomaterials are strong fluorescence quenchers, correlations among adsorption efficiency, quenching efficiency, and FP need to be interpreted carefully. In this work, carboxyfluorescein (FAM)-labeled DNA oligonucleotides were studied under various quenching conditions. First, quenching was induced by lowering the pH, taking advantage of the fact that FAM is almost nonfluorescent at a pH below 4. Strong interactions were observed between the FAM label and polyadenine DNA, as judged by the increased FP at low pH, while FAM-labeled polythymine DNA was less affected by the pH. Comparisons were also performed with FAM-labeled poly(ethylene glycol) and bovine serum albumin. An equation was derived to calculate the effect of fluorescence quenching and DNA adsorption by nanomaterials. For strongly quenching nanomaterials, such as graphene oxide, DNA adsorption alone does not change the measured FP. Light scattering and weak fluorescence from graphene oxide increase FP in these cases. For comparison, a strongly adsorbing but weak quenching material, Y₂O₃, was also studied and the result was consistent with a normal binding reaction. Overall, FP is a powerful technique for binding and adsorption assays, but quenched samples need to be interpreted with care.