Genetically Encoded Protease Substrate Based on Lanthanide-Binding Peptide for Time-Gated Fluorescence Detection

Switch-on Fluorescence Analysis of Protease Activity with the Assistance of a Nickel Ion-Nitrilotriacetic Acid-Conjugated Magnetic Nanoparticle

Heterogeneous protease biosensors show high sensitivity and selectivity but usually require the immobilization of peptide substrates on a solid interface. Such methods exhibit the disadvantages of complex immobilization steps and low enzymatic efficiency induced by steric hindrance. In this work, we proposed an immobilization-free strategy for protease detection with high simplicity, sensitivity and selectivity. Specifically, a single-labeled peptide with oligohistidine-tag (His-tag) was designed as the protease substrate, which can be captured by a nickel ion-nitrilotriacetic acid (Ni-NTA)-conjugated magnetic nanoparticle (MNP) through the coordination interaction between His-tag and Ni-NTA. When the peptide was digested by protease in a homogeneous solution, the signal-labeled segment was released from the substrate. The unreacted peptide substrates could be removed by Ni-NTA-MNP, and the released segments remained in solution to emit strong fluorescence. The method was used to determine protease of caspase-3 with a low detection limit (4 pg/mL). By changing the peptide sequence and signal reporters, the proposal could be used to develop novel homogeneous biosensors for the detection of other proteases.

Luminescent Lifetime Regulation of Lanthanide-Doped Nanoparticles for Biosensing

Lanthanide-doped nanoparticles possess numerous advantages including tunable luminescence emission, narrow peak width and excellent optical and thermal stability, especially concerning the long lifetime from microseconds to milliseconds. Differing from other shorter-lifetime fluorescent nanomaterials, the long lifetime of lanthanide-doped nanomaterials is independent with background fluorescence interference and biological tissue depth. This review presents the recent advances in approaches to regulating the lifetime and applications of bioimaging and biodetection. We begin with the introduction of the strategies for regulating the lifetime by modulating the core-shell structure, adjusting the concentration of sensitizer and emitter, changing energy transfer channel, establishing a fluorescence resonance energy transfer pathway and changing temperature. We then summarize the applications of these nanoparticles in biosensing, including ion and molecule detecting, DNA and protease detection, cell labeling, organ imaging and thermal and pH sensing. Finally, the prospects and challenges of the lanthanide lifetime regulation for fundamental research and practical applications are also discussed.

Miniaturized bioluminescence technology for single-cell quantification of caspase-3/7

Correct determination of the instantaneous level and changes of relevant proteins inside individual cells is essential for correct interpretation and understanding of physiological, diagnostic, and therapeutic events. Thus, single-cell analyses are important for quantification of natural cellular heterogeneity, which cannot be evaluated from averaged data of a cell population measurements. Here, we developed an original highly sensitive and selective instrumentation and methodology based on homogeneous single-step bioluminescence assay to quantify caspases and evaluate their heterogeneity in individual cells. Individual suspended cells are selected under microscope and reliably transferred into the 7 µl detection vials by a micromanipulator. The sensitivity of the method is given by implementation of photomultiplying tube with a cooled photocathode working in the photon counting mode. By optimization of our device and methodology, the limits of detection and quantitation were decreased down to 2.1 and 7.0 fg of recombinant caspase-3, respectively. These masses are lower than average amounts of caspase-3/7 in individual apoptotic and even non-apoptotic cells. As a proof of concept, the content of caspase-3/7 in single treated and untreated HeLa cells was determined to be 154 and 25 fg, respectively. Based on these results, we aim to use the technology for investigations of non-apoptotic functions of caspases.

Interaction of Cucurbit[7]uril With Protease Substrates: Application to Nanosecond Time-Resolved Fluorescence Assays

We report the use of the macrocyclic host cucurbit[7]uril (CB7) as a supramolecular additive in nanosecond time-resolved fluorescence (Nano-TRF) assays for proteases to enhance the discrimination of substrates and products and, thereby, the sensitivity. A peptide substrate was labeled with 2,3-diazabicyclo[2.2.2]oct-2-ene (DBO) as a long-lived (>300 ns) fluorescent probe and 3-nitrotyrosine was established as a non-fluorescent fluorescence resonance energy transfer (FRET) acceptor that acts as a “dark quencher.” The substrate was cleaved by the model proteases trypsin and chymotrypsin and the effects of the addition of CB7 to the enzyme assay mixture were investigated in detail using UV/VIS absorption as well as steady-state and time-resolved fluorescence spectroscopy. This also allowed us to identify the DBO and nitrotyrosine residues as preferential binding sites for CB7 and suggested a hairpin conformation of the peptide, in which the guanidinium side chain of an arginine residue is additionally bound to a vacant ureido rim of one of the CB7 hosts.

Preparation of a DNA-Tb-MOF conjugate as a time-resolved probe for the detection of SO2 derivatives through an off-on effect

Herein we synthesize a DNA-sensitized Tb-MOF conjugate (DNA-Tb-MOF) as a time-resolved luminescent probe to sensitively and selectively assay SO₂ and their derivatives (i.e., HSO₃^-) through a photoluminescence off-on effect. The charge and energy transfer mechanism enables the demonstration of the effect of the photoluminescence turn-on which results from the reaction between the amino group of the DNA-Tb-MOF conjugate and SO₂/HSO₃^-. The results demonstrate that the DNA-Tb-MOF conjugate probe can sense SO₂ and their derivatives (i.e., HSO₃^-) with a detection limit of 0.02 ppm. Moreover, the photoluminescence off-on effect can be observed even by the naked eye.

The Marriage of Protein and Lanthanide: Unveiling a Time-Resolved Fluorescence Sensor Array Regulated by pH toward High-Throughput Assay of Metal Ions in Biofluids

A protein/lanthanide complex (BSA/Tb³⁺)-based sensor array in two different pH buffers has been designed for high-throughput recognition and time-resolved fluorescence (TRF) detection of metal ions in biofluids. BSA, which acted as an antenna ligand, can sensitize the fluorescence of Tb³⁺ (i.e., antenna effect), while the presence of metal ions would lead to the corresponding conformational change of BSA for altering the antenna effect accompanied by a substantial TRF performance of Tb³⁺. This principle has also been fully proved by both experimental characterizations and coarse-grained molecular dynamics (CG-MD) studies. By using Tris-HCl buffer with different pHs (at 7.4 and 8.5), 17 metal ions have been well-distinguished by using our proposed BSA/Tb³⁺ sensor array. Moreover, the sensor array has the potential to discriminate different concentrations of the same metal ions and a mixture of metal ions. Remarkably, the detection of metal ions in biofluids can be realized by utilizing the presented sensor array, verifying its practical applications. The platform avoids the synthesis of multiplex sensing receptors, providing a new method for the construction of convenient and feasible lanthanide complex-based TRF sensing arrays.

Application of lanthanide luminescence in probing enzyme activity

Enzymes play critical roles in the regulation of cellular function and are implicated in numerous disease conditions. Reliable and practicable assays are required to study enzyme activity, to facilitate the discovery of inhibitors and activators of enzymes related to disease. In recent years, a variety of enzyme assays have been devised that utilise luminescent lanthanide(iii) complexes, taking advantage of their high detection sensitivities, long luminescence lifetimes, and line-like emission spectra that permit ratiometric and time-resolved analyses. In this Feature article, we focus on recent progress in the development of enzyme activity assays based on lanthanide(iii) luminescence, covering a variety of strategies including Ln(iii)-labelled antibodies and proteins, Ln(iii) ion encapsulation within defined peptide sequences, reactivity-based Ln(iii) probes, and discrete Ln(iii) complexes. Emerging approaches for monitoring enzyme activity are discussed, including the use of anion responsive lanthanide(iii) complexes, capable of molecular recognition and luminescence signalling of polyphosphate anions.

A Label-free Time-resolved Luminescent Platform for Sensitive Endonuclease V Detection Based on Exonuclease III Regulated DNA-Tb3+ Luminescence

Endonuclease V (EndoV) plays the important role of nucleotide excision repair (NER) in the maintenance of genomic stability. Highly sensitive detection of EndoV was achieved through an oligonucleotides sensitizing Tb³⁺ luminescent technique. We found that although both guanine-rich (G-rich) single-stranded DNA and dGMP could enhance the time-resolved luminescence of Tb³⁺, their efficiencies of enhancement were considerably different. Employing such interesting phenomenon, a label-free and time-resolved luminescent strategy for the sensitive detection of EndoV activity was developed based on DNA-enhanced time-resolved luminescence (TRL) of Tb³⁺. The EndoV was used to cut off the deoxyinosine site (dI) and convert the 3'-protruding termini to a recessed end, and Exonuclease III (Exo III) was used to enhance the signal contrast via digestion of G-rich DNA to dNTP. Combining with the natural advantages of the TRL, the proposed method exhibited a good linear response to EndoV ranging from 0.005 to 0.4 U/mL, with a low limit of detection of 0.005 U/mL.

A label-free and time-resolved luminescence strategy for the detection of proteins based on DNA-Tb(3+) luminescence quenched by graphene oxide

A sensitive, label-free and time-resolved luminescent aptasensor to detect proteins was developed based on the DNA-enhanced time-resolved luminescence of Tb(3+) and graphene oxide (GO). We found that the DNA no matter with a G-quadruplex structure or not could greatly enhance the long-lived emission of Tb(3+), and the luminescence of DNA-Tb(3+) could be effectively quenched by GO after the DNA-Tb(3+) was adsorbed onto GO. The target protein combined with an aptamer to form a protein/DNA complex restrained the quenching of DNA-Tb(3+) emission by GO. Thrombin and a 29-mer anti-thrombin aptamer were employed as a model analyte and a recognition element. There is a good linear relationship between the aptamer-Tb(3+) complex luminescence with the thrombin concentrations of 1 to 100 nM with a low detection limit of 0.8 nM. Since the time-resolved luminescence can eliminate the unspecific background fluorescence, the proposed aptasensor has been successfully applied in complicated biological samples for thrombin detection. This novel strategy presents a potential universal method for detection of other molecules.

Application of inductively coupled plasma mass spectrometry in the study of apoptosis: determination of caspase-3 using a gold nanoparticle tag

Apoptosis is a main type of cell death in which caspase-3 plays a key role. In this work, a simple, fast and sensitive immunoassay for caspase-3 is established by using inductively coupled plasma mass spectrometry (ICP-MS) detection and signal enhancement gold nanoparticle (Au-NP) labelling of the secondary antibody (IgG). After the immunoreaction of caspase-3, primary antibody and Au-NP labeled IgG, the concentration of caspase-3 was determined by ICP-MS analysis of the Au-NPs released from the immunocomplex. Under the optimized conditions, a limit of detection (LOD, 3σ) of 0.42 ng mL(-1) (0.31 nM) was obtained for caspase-3, with a dynamic range of 1-200 ng mL(-1) and a relative standard deviation of 4.1% (c = 5 ng mL(-1), n = 11). The proposed method has good specificity towards caspase-3. To demonstrate the application potential of the proposed method, the cell lysates of Hg(2+)-induced HepG2 cells were analyzed, and it was found that the concentration of caspase-3 increased when increasing the incubation concentration of Hg(2+). This method is easy, sensitive and selective, and has excellent capability of tolerating a complex biological matrix, indicating the potential of the ICP-MS-based assay in the study of apoptosis.

Small Molecule Active Site Directed Tools for Studying Human Caspases

Caspases are proteases of clan CD and were described for the first time more than two decades ago. They play critical roles in the control of regulated cell death pathways including apoptosis and inflammation. Due to their involvement in the development of various diseases like cancer, neurodegenerative diseases, or autoimmune disorders, caspases have been intensively investigated as potential drug targets, both in academic and industrial laboratories. This review presents a thorough, deep, and systematic assessment of all technologies developed over the years for the investigation of caspase activity and specificity using substrates and inhibitors, as well as activity based probes, which in recent years have attracted considerable interest due to their usefulness in the investigation of biological functions of this family of enzymes.

Multicolored, Tb³⁺-Based Antibody-Free Detection of Multiple Tyrosine Kinase Activities

Kinase signaling is a major mechanism driving many cancers. While many inhibitors have been developed and are employed in the clinic, resistance due to crosstalk and pathway reprogramming is an emerging problem. High-throughput assays to detect multiple pathway kinases simultaneously could better model these complex relationships and enable drug development to combat this type of resistance. We developed a strategy to take advantage of time-resolved luminescence of Tb(3+)-chelated phosphotyrosine-containing peptides, which facilitated efficient energy transfer to small molecule fluorophores conjugated to the peptides to produce orthogonally colored biosensors for two different kinases. This enabled multiplexed detection with high signal-to-noise in a high-throughput-compatible format. This proof-of-concept study provides a platform that could be applied to other lanthanide metal and fluorophore combinations to achieve even greater multiplexing without the need for phosphospecific antibodies.

Persistent luminescence nanoprobe for biosensing and lifetime imaging of cell apoptosis via time-resolved fluorescence resonance energy transfer

Time-resolved fluorescence technique can reduce the short-lived background luminescence and auto-fluorescence interference from cells and tissues by exerting the delay time between pulsed excitation light and signal acquisition. Here, we prepared persistent luminescence nanoparticles (PLNPs) to design a universal time-resolved fluorescence resonance energy transfer (TR-FRET) platform for biosensing, lifetime imaging of cell apoptosis and in situ lifetime quantification of intracellular caspase-3. Three kinds of PLNPs-based nanoprobes are assembled by covalently binding dye-labeled peptides or DNA to carboxyl-functionalized PLNPs for the efficient detection of caspase-3, microRNA and protein. The peptides-functionalized nanoprobe is also employed for fluorescence lifetime imaging to monitor cell apoptosis, which shows a dependence of cellular fluorescence lifetime on caspase-3 activity and thus leads to an in situ quantification method. This work provides a proof-of-concept for PLNPs-based TR-FRET analysis and demonstrates its potential in exploring dynamical information of life process.

Chemiluminescent detection of cell apoptosis enzyme by gold nanoparticle-based resonance energy transfer assay

We report a new chemiluminescence resonance energy transfer (CRET) technique, using gold nanoparticles (AuNPs) as efficient energy acceptor, for homogeneous measurement of cell apoptosis enzyme with high sensitivity. In the design of the CRET system, we chose the highly sensitive chemiluminescence (CL) reaction between luminol and hydrogen peroxide catalysed by horseradish peroxidase (HRP) because the CL spectrum of luminol (λ max 425 nm) partially overlaps the visible absorption bands of AuNPs. In this system, the peptide substrate (DEVD) of caspase 3 was linked to the AuNP surface by Au-S linkage. HRP was attached to the AuNP surface by means of a bridge formed by the streptavidin-biotin reaction. CRET occurred as a result of formation of AuNP-peptide-biotin-streptavidin-HRP complexes. The CL of luminol was significantly reduced, because of the quenching effect of AuNPs. The quenched CL was recovered after cleavage of DEVD by caspase 3, an enzyme involved in the apoptotic process. Experimental conditions were systematically investigated. Under the optimum conditions the increase of the CL signal was linearly dependent on caspase 3 concentration within the concentration range 25 pmol L(-1) to 800 pmol L(-1) and the detection limit of caspase 3 was as low as 20 pmol L(-1), one order of magnitude lower than for FRET sensors based on graphene oxides. Our method was successfully used to detect drug-induced apoptosis of cells. This approach is expected to be extended to other assays, i.e., using other enzymes, analytes, CL substances, and even other nanoparticles (e.g., quantum dots and graphene).

FITC-quencher based caspase 3-activatable nanoprobes for effectively sensing caspase 3 in vitro and in cells

By employing fluorescence resonance energy transfer (FRET) quenching, we rationally designed two new FITC-quencher based nanoprobes for effectively sensing caspase 3 (Casp3) in vitro and in cells. Our nanoprobes hold promise for assessing the chemotherapeutic effect of cancer treatment.

N,N-dimethyldodecylamine oxide self-organization in the presence of lanthanide ions in aqueous and aqueous-decanol solutions

The article represents the results of research in self-organization of new lanthanide systems in water-decanol medium. The systems are based on N,N-dimethyldodecylamine oxide, a zwitterionic surfactant. The study covers the complex formation of lanthanide ions with C12DMAO molecules and the influence of Ln(III) ions and medium composition on surfactant association in diluted solutions. The analysis of adsorption isotherms was carried out on the basis of the combination of Gibbs and Langmuir adsorption equations. The results were used to determine physicochemical properties and parameters of a monomolecular adsorption layer. The research objects were various lanthanide ions with identical coordination centers. A number of spectroscopic methods (UV, NMR self-diffusion, EPR, dynamic light scattering (DLS), and fluorescent analysis) were involved in the research for comparative estimations of molecular dynamics, critical micellization concentration, geometry, sizes, and aggregation numbers of micellar aggregates. Micelle structure simulation revealed good agreement between experimental data and quantum chemical calculations.