Self-designed portable dual-mode fluorescence device with custom python-based analysis software for rapid detection via dual-color FRET aptasensor with IoT capabilities.

An innovative aptasensor incorporating MoS2-modified bicolor quantum dots and a portable spectrometer, designed for the simultaneous detection of ochratoxin A (OTA) and aflatoxin B1 (AFB1) in corn was developed. Carbon dots and CdZnTe quantum dots were as nano-donors to label OTA and AFB1 aptamers, respectively. These labeled aptamers were subsequently attached to MoS2 receptors, enabling fluorescence resonance energy transfer (FRET). With targets, the labeled aptamers detached from the nano-donors, thereby disrupting the FRET process and resulting in fluorescence recovery. Furthermore, a portable dual-mode fluorescence detection system, complemented with customized python-based analysis software, was developed to facilitate rapid and convenient detection using this dual-color FRET aptasensor. The developed host program is connected to the spectrometer and transmits data to the cloud, enabling the device to have Internet of Things (IoT) characteristics. Connected to the cloud, this IoT-enabled device offers convenient and reliable fungal toxin detection for food safety.

One-step hydrothermal synthesis of WS2 quantum dots as fluorescent sensor for sensitive and selective recognition of hemoglobin and cardiac biomarker myoglobin.

Transition metal dichalcogenide (TMD) dots exhibit excellent photoluminescence performance due to the quantum confinement effect and edge effect, and are extensively applied in electronic and optical devices, sensors, catalysis, and bioimaging. In this work, WS2 quantum dots (WS2 QDs) were prepared under a simple one-step hydrothermal method by optimizing the reaction conditions, and a quantum yield of 11.23% was achieved. The as-prepared WS2 QDs possess good photo-bleaching resistance, salt tolerance, and pH stability. The fluorescence investigations showed that the WS2 QDs acted as a highly efficient fluorescent sensor to detect hemoglobin (Hb) and cardiac biomarker myoglobin (Myo). The linear range was 1-600 µg/mL for Hb and 0.01-120 µg/mL for Myo, with detection limits as low as 260 and 7.6 ng/mL, respectively. Importantly, the WS2 QDs were used to determine the Hb/Myo content in human blood/serum samples, with satisfactory results, indicating that this technique holds promise for application in clinical diagnosis associated with Hb/Myo levels. To the best of our knowledge, this is the first example of TMD QDs without any modification as a fluorescent sensor for detecting Hb and Myo simultaneously.

2D Material-Based Optical Biosensor: Status and Prospect.

The combination of 2D materials and optical biosensors has become a hot research topic in recent years. Graphene, transition metal dichalcogenides, black phosphorus, MXenes, and other 2D materials (metal oxides and degenerate semiconductors) have unique optical properties and play a unique role in the detection of different biomolecules. Through the modification of 2D materials, optical biosensor has the advantages that traditional sensors (such as electrical sensing) do not have, and the sensitivity and detection limit are greatly improved. Here, optical biosensors based on different 2D materials are reviewed. First, various detection methods of biomolecules, including surface plasmon resonance (SPR), fluorescence resonance energy transfer (FRET), and evanescent wave and properties, preparation and integration strategies of 2D material, are introduced in detail. Second, various biosensors based on 2D materials are summarized. Furthermore, the applications of these optical biosensors in biological imaging, food safety, pollution prevention/control, and biological medicine are discussed. Finally, the future development of optical biosensors is prospected. It is believed that with their in-depth research in the laboratory, optical biosensors will gradually become commercialized and improve people's quality of life in many aspects.

ABEL-FRET: tether-free single-molecule FRET with hydrodynamic profiling.

Single-molecule Förster resonance energy transfer (smFRET) has become a versatile and widespread method to probe nanoscale conformation and dynamics. However, current experimental modalities often resort to molecule immobilization for long observation times and do not always approach the resolution limit of FRET-based nanoscale metrology. Here we present ABEL-FRET, an immobilization-free platform for smFRET measurements with ultrahigh resolving power in FRET efficiency. Importantly, single-molecule diffusivity is used to provide additional size and shape information for hydrodynamic profiling of individual molecules, which, together with the concurrently measured intramolecular conformation through FRET, enables a holistic and dynamic view of biomolecules and their complexes.

Temporal analysis of T-cell receptor-imposed forces via quantitative single molecule FRET measurements.

Mechanical forces acting on ligand-engaged T-cell receptors (TCRs) have previously been implicated in T-cell antigen recognition, yet their magnitude, spread, and temporal behavior are still poorly defined. We here report a FRET-based sensor equipped either with a TCR-reactive single chain antibody fragment or peptide-loaded MHC, the physiological TCR-ligand. The sensor was tethered to planar glass-supported lipid bilayers (SLBs) and informed most directly on the magnitude and kinetics of TCR-imposed forces at the single molecule level. When confronting T-cells with gel-phase SLBs we observed both prior and upon T-cell activation a single, well-resolvable force-peak of approximately 5 pN and force loading rates on the TCR of 1.5 pN per second. When facing fluid-phase SLBs instead, T-cells still exerted tensile forces yet of threefold reduced magnitude and only prior to but not upon activation.

A turn-on upconversion fluorescence sensor for acrylamide in potato chips based on fluorescence resonance energy transfer and thiol-ene Michael addition.

This study describes a turn-on upconversion fluorescence sensor for the detection of acrylamide (AA) based on glutathione (GSH) modulated turn-on fluorescence strategy. Polyethyleneimine-modified upconversion nanoparticles were first prepared by the hydrothermal method and then Rhodamine B derivative (RBD) was loaded on their surface through non-covalent bonding. The GSH coupled with RBD and strongly quenched the upconversion fluorescence via fluorescence resonance energy transfer. Upon addition of tris (2-carboxyethyl) phosphine, the thiol-ene Michael addition reaction between GSH and AA was efficiently catalyzed, resulted in the quenched fluorescence triggered on. Under the optimum conditions, a linear detection range from 0.1 to 104 µM was implemented for AA with a limit of detection of 0.68 nM and great sensitivity was observed. Importantly, the proposed sensor was evaluated for spiked potato chips samples with a satisfactory result in contrast to high-performance liquid chromatography, confirmed its applicability for the rapid detection of AA.

Metallothionein dimerization evidenced by QD-based Förster resonance energy transfer and capillary electrophoresis.

Herein, we report a new simple and easy-to-use approach for the characterization of protein oligomerization based on fluorescence resonance energy transfer (FRET) and capillary electrophoresis with LED-induced detection. The FRET pair consisted of quantum dots (QDs) used as an emission tunable donor (emission wavelength of 450 nm) and a cyanine dye (Cy3), providing optimal optical properties as an acceptor. Nonoxidative dimerization of mammalian metallothionein (MT) was investigated using the donor and acceptor covalently conjugated to MT. The main functions of MTs within an organism include the transport and storage of essential metal ions and detoxification of toxic ions. Upon storage under aerobic conditions, MTs form dimers (as well as higher oligomers), which may play an essential role as mediators in oxidoreduction signaling pathways. Due to metal bridging by Cd2+ ions between molecules of metallothionein, the QDs and Cy3 were close enough, enabling a FRET signal. The FRET efficiency was calculated to be in the range of 11-77%. The formation of MT dimers in the presence of Cd2+ ions was confirmed by MALDI-MS analyses. Finally, the process of oligomerization resulting in FRET was monitored by CE, and oligomerization of MT was confirmed.

Engineering with NanoLuc: a playground for the development of bioluminescent protein switches and sensors.

The small engineered luciferase NanoLuc has rapidly become a powerful tool in the fields of biochemistry, chemical biology, and cell biology due to its exceptional brightness and stability. The continuously expanding NanoLuc toolbox has been employed in applications ranging from biosensors to molecular and cellular imaging, and currently includes split complementation variants, engineering techniques for spectral tuning, and bioluminescence resonance energy transfer-based concepts. In this review, we provide an overview of state-of-the-art NanoLuc-based sensors and switches with a focus on the underlying protein engineering approaches. We discuss the advantages and disadvantages of various strategies with respect to sensor sensitivity, modularity, and dynamic range of the sensor and provide a perspective on future strategies and applications.

A FRET-ICT Dual-Modulated Ratiometric Fluorescence Sensor for Monitoring and Bio-Imaging of Cellular Selenocysteine.

Since the fluctuation of cellular selenocysteine (Sec) concentration plays an all-important role in the development of numerous human disorders, the real-time fluorescence detection of Sec in living systems has attracted plenty of interest during the past decade. In order to obtain a faster and more sensitive small organic molecule fluorescence sensor for the Sec detection, a new ratiometric fluorescence sensor Q7 was designed based on the fluorescence resonance energy transfer (FRET) strategy with coumarin fluorophore as energy donor and 4-hydroxy naphthalimide fluorophore (with 2,4-dinitrobenzene sulfonate as fluorescence signal quencher and Sec-selective recognition site) as an energy acceptor. The sensor Q7 exhibited only a blue fluorescence signal, and displayed two well distinguished emission bands (blue and green) in the presence of Sec with ∆λ of 68 nm. Moreover, concentrations ranging of quantitative detection of Sec of Q7 was from 0 to 45 µM (limit of detection = 6.9 nM), with rapid ratiometric response, high sensitivity and selectivity capability. Impressively, the results of the living cell imaging test demonstrated Q7 has the potentiality of being an ideal sensor for real-time Sec detection in biosystems.

Automated and optimally FRET-assisted structural modeling.

FRET experiments can provide state-specific structural information of complex dynamic biomolecular assemblies. However, to overcome the sparsity of FRET experiments, they need to be combined with computer simulations. We introduce a program suite with (i) an automated design tool for FRET experiments, which determines how many and which FRET pairs should be used to minimize the uncertainty and maximize the accuracy of an integrative structure, (ii) an efficient approach for FRET-assisted coarse-grained structural modeling, and all-atom molecular dynamics simulations-based refinement, and (iii) a quantitative quality estimate for judging the accuracy of FRET-derived structures as opposed to precision. We benchmark our tools against simulated and experimental data of proteins with multiple conformational states and demonstrate an accuracy of ~3 Å RMSDCα against X-ray structures for sets of 15 to 23 FRET pairs. Free and open-source software for the introduced workflow is available at https://github.com/Fluorescence-Tools . A web server for FRET-assisted structural modeling of proteins is available at http://nmsim.de .

NIR-II bioluminescence for in vivo high contrast imaging and in situ ATP-mediated metastases tracing.

Bioluminescence imaging has been widely used in life sciences and biomedical applications. However, conventional bioluminescence imaging usually operates in the visible region, which hampers the high-performance in vivo optical imaging due to the strong tissue absorption and scattering. To address this challenge, here we present bioluminescence probes (BPs) with emission in the second near infrared (NIR-II) region at 1029 nm by employing bioluminescence resonance energy transfer (BRET) and two-step fluorescence resonance energy transfer (FRET) with a specially designed cyanine dye FD-1029. The biocompatible NIR-II-BPs are successfully applied to vessels and lymphatics imaging in mice, which gives ~5 times higher signal-to-noise ratios and ~1.5 times higher spatial resolution than those obtained by NIR-II fluorescence imaging and conventional bioluminescence imaging. Their capability of multiplexed imaging is also well displayed. Taking advantage of the ATP-responding character, the NIR-II-BPs are able to recognize tumor metastasis with a high tumor-to-normal tissue ratio at 83.4.

Fast three-color single-molecule FRET using statistical inference.

We describe theory, experiments, and analyses of three-color Förster resonance energy transfer (FRET) spectroscopy for probing sub-millisecond conformational dynamics of protein folding and binding of disordered proteins. We devise a scheme that uses single continuous-wave laser excitation of the donor instead of alternating excitation of the donor and one of the acceptors. This scheme alleviates photophysical problems of acceptors such as rapid photobleaching, which is crucial for high time resolution experiments with elevated illumination intensity. Our method exploits the molecular species with one of the acceptors absent or photobleached, from which two-color FRET data is collected in the same experiment. We show that three FRET efficiencies and kinetic parameters can be determined without alternating excitation from a global maximum likelihood analysis of two-color and three-color photon trajectories. We implement co-parallelization of CPU-GPU processing, which leads to a significant reduction of the likelihood calculation time for efficient parameter determination.

Measuring Interactions Between Tau and Aggregation Inducers with Single-Molecule Förster Resonance Energy Transfer.

Tau is an intrinsically disordered protein implicated in the pathogenesis of Alzheimer's disease and other neurodegenerative disorders. Here we describe the application of single-molecule Förster resonance energy transfer (smFRET) for the characterization of the interactions between tau and polyphosphate, an intracellular polymer that accelerates tau aggregation. We describe the design of tau constructs, purification and fluorescent labeling of tau, and details of acquisition and analysis of smFRET data. The protocols provided here outline an approach that may be applied to the study of other intrinsically disordered proteins and their binding partners.

Live-Cell FRET Imaging of Phosphorylation-Dependent Caveolin-1 Switch.

The detection of dynamic conformational changes in proteins in live cells is challenging. Live-cell FRET (Förster Resonance Energy Transfer) is an example of a noninvasive technique that can be used to achieve this goal at nanometer resolution. FRET-based assays are dependent on the presence of fluorescent probes, such as CFP- and YFP-conjugated protein pairs. Here, we describe an experimental protocol in which live-cell FRET was used to measure conformational changes in caveolin-1 (Cav-1) oligomers on the surface of plasmalemma vesicles, or caveolae.

Flow Chamber Assay to Image the Response of FRET-Based Nanosensors in Pollen Tubes to Changes in Medium Composition.

Pollen tubes growing in the transmitting tract are presented with an extracellular matrix rich in a variety of substances. The expression of a multitude of genes for transport proteins in the pollen tube indicates that pollen tubes take up at least some of the components provided by the transmitting tract, for example nutrients, ions, or signaling molecules. FRET (Förster resonance energy transfer)-based nanosensors are perfectly suited to study the uptake of these molecules into pollen tubes. They are genetically encoded and can easily be expressed in Arabidopsis pollen tubes. Furthermore, the method is noninvasive and nanosensors for a wide range of substances are available. This chapter will describe the design of plasmids required to generate stable Arabidopsis lines with a pollen tube-specific expression of nanosensor constructs. We also present a method to germinate Arabidopsis pollen tubes in a flow chamber slide that allows the perfusion of the pollen tubes with liquid medium supplemented with the substrate of the nanosensor. Simultaneous evaluation of the FRET efficiency of the nanosensor by confocal microscopy reveals whether the substance is taken up by the pollen tubes. Together with the great number of available nanosensors this method can generate a detailed picture of the substances that are taken up during pollen tubes growth.

Adaptive optics for a time-resolved Förster resonance energy transfer (FRET) and fluorescence lifetime imaging microscopy (FLIM) in vivo.

Förster resonance energy transfer (FRET) and fluorescence lifetime imaging (FLIM) have been coupled with multiphoton microscopy to image in vivo dynamics. However, the increase in optical aberrations as a function of depth significantly reduces the fluorescent signal, spatial resolution, and fluorescence lifetime accuracy. We present the development of a time-resolved FRET-FLIM imaging system with adaptive optics. We demonstrate the improvement of our adaptive optics (AO)-FRET-FLIM instrument over standard multiphoton FRET-FLIM imaging. We validate our approach using fixed cellular samples with FRET standards and in vivo with live imaging in a mouse kidney.

Quantitative real-time imaging of intracellular FRET biosensor dynamics using rapid multi-beam confocal FLIM.

Fluorescence lifetime imaging (FLIM) is a quantitative, intensity-independent microscopical method for measurement of diverse biochemical and physical properties in cell biology. It is a highly effective method for measurements of Förster resonance energy transfer (FRET), and for quantification of protein-protein interactions in cells. Time-domain FLIM-FRET measurements of these dynamic interactions are particularly challenging, since the technique requires excellent photon statistics to derive experimental parameters from the complex decay kinetics often observed from fluorophores in living cells. Here we present a new time-domain multi-confocal FLIM instrument with an array of 64 visible beamlets to achieve parallelised excitation and detection with average excitation powers of ~ 1-2 µW per beamlet. We exemplify this instrument with up to 0.5 frames per second time-lapse FLIM measurements of cAMP levels using an Epac-based fluorescent biosensor in live HeLa cells with nanometer spatial and picosecond temporal resolution. We demonstrate the use of time-dependent phasor plots to determine parameterisation for multi-exponential decay fitting to monitor the fractional contribution of the activated conformation of the biosensor. Our parallelised confocal approach avoids having to compromise on speed, noise, accuracy in lifetime measurements and provides powerful means to quantify biochemical dynamics in living cells.

Nanococktail Based on AIEgens and Semiconducting Polymers: A Single Laser Excited Image-Guided Dual Photothermal Therapy.

Semiconducting polymers (SPs)-based dual photothermal therapy (PTT) obtained better therapeutic effect than single PTT due to its higher photothermal conversion efficiency. However, most dual PTT need to use two lasers for heat generation, which brings about inconvenience and limitation to the experimental operations. Herein, we report the development of "nanococktail" nanomaterials (DTPR) with 808 nm-activated image-guided dual photothermal properties for optimized cancer therapy. Methods: In this work, we co-encapsulated AIEgens (TPA-BDTO, T) and SPs (PDPPP, P) by using maleimide terminated amphiphilic polymer (DSPE-PEG2000-Mal, D), then further conjugated the targeting ligands (RGD, R) through "click" reaction. Finally, such dual PTT nanococktail (termed as DTPR) was constructed. Results: Once DTPR upon irradiation with 808 nm laser, near-infrared fluorescence from T could be partially converted into thermal energy through fluorescence resonance energy transfer (FRET) between T and P, coupling with the original heat energy generated by the photothermal agent P itself, thus resulting in image-guided dual PTT. The photothermal conversion efficiency of DTPR reached 60.3% (dual PTT), much higher as compared to its inherent photothermal effect of only 31.5% (single PTT), which was further proved by the more severe photothermal ablation in vitro and in vivo upon 808 nm laser irradiation. Conclusion: Such smart "nanococktail" nanomaterials could be recognized as a promising photothermal nanotheranostics for image-guided cancer treatment.

Multi-Stimuli Responsive FRET Processes of Bifluorophoric AIEgens in an Amphiphilic Copolymer and Its Application to Cyanide Detection in Aqueous Media.

A novel amphiphilic aggregation-induced emission (AIE) copolymer, that is, poly(NIPAM-co-TPE-SP), consisting of N-isopropylacrylamide (NIPAM) as a hydrophilic unit and a tetraphenylethylene-spiropyran monomer (TPE-SP) as a bifluorophoric unit is reported. Upon UV exposure, the close form of non-emissive spiropyran (SP) in poly(NIPAM-co-TPE-SP) can be photo-switched to the open form of emissive merocyanine (MC) in poly(NIPAM-co-TPE-MC) in an aqueous solution, leading to ratiometric fluorescence of AIEgens between green TPE and red MC emissions at 517 and 627 nm, respectively, via Förster resonance energy transfer (FRET). Distinct FRET processes of poly(NIPAM-co-TPE-MC) can be observed under various UV and visible light irradiations, acid-base conditions, thermal treatments, and cyanide ion interactions, which are also confirmed by theoretical studies. The subtle perturbations of environmental factors, such as UV exposure, pH value, temperature, and cyanide ion, can be detected in aqueous media by distinct ratiometric fluorescence changes of the FRET behavior in the amphiphilic poly(NIPAM-co-TPE-MC). Moreover, the first FRET sensor polymer poly(NIPAM-co-TPE-MC) based on dual AIEgens of TPE and MC units is developed to show a very high selectivity and sensitivity with a low detection limit (LOD = 0.26 µM) toward the cyanide ion in water, which only contain an approximately 1% molar ratio of the bifluorophoric content and can be utilized in cellular bioimaging applications for cyanide detections.

MicroRNAs in ovarian cancer and recent advances in the development of microRNA-based biosensors.

Ovarian cancer is the most aggressive of all gynaecological malignancies and is the leading cause of cancer-associated mortality worldwide. Over the recent years, there has been a sharp increase in this mortality rate, mostly due to late diagnosis, which can be attributed to the lack of an early and specific biomarker. Under this scenario, recent interest has shifted towards ovarian cancer associated miRNAs which play strong regulatory roles in various cellular processes. miRNAs have emerged as promising non/minimally invasive cancer biomarkers for improved diagnostic, prognostic and streamlined therapeutic applications. A large number of miRNA assays have been reported that are based on nucleic acid detection-based techniques such as RT-qPCR, microarrays and RNA sequencing methods. Despite demonstrating commendable analytical performances, these laboratory-based techniques are expensive and hence not ideally suited for routine use in resource-limited settings. In recent years, considerable attention has been dedicated to the development of relatively simple, rapid and inexpensive miRNA biosensor strategies. Among these, electrochemical sensors have shown a great promise towards point-of-care diagnostics, due to their inherent advantages such as simplicity, sensitivity, amenability to high levels of multiplexing as well as low cost. In this paper, we provide an overview of the potential role of miRNAs in ovarian cancer, as well as recent advances in the development of nanotechnology-based, optical, and electrochemical biosensing-strategies for miRNA detection.