Chapter 1 Förster resonance energy transfer—FRET what is it, why do it, and how it's done

Vibrational effects on polarizability: insights from normal mode analysis

The performance of sensing and optical devices is closely linked to the molecular polarizability response, a property significantly influenced by the polarizability tensor's isotropic and anisotropic components. In this study, we investigate the impact of vibrational motion on polarizability. We analyze how intramolecular vibrations affect the polar properties of molecules commonly employed in refrigerants and gas detection technologies. Our computational estimates align well with experimental data. It is revealed that vibrational effects can introduce uncertainties of up to 6% in sensing devices and 50% in optical devices due to nuclear oscillations. Furthermore, normal mode analysis highlights specific vibrational modes that enhance molecular polarizability.

Cooling-Induced Order-Disorder Phase Transition in CsPbBr3 Nanocrystal Superlattices

Perovskite nanocrystal superlattices are being actively studied after reports have emerged on collective excitonic properties at cryogenic temperatures, where energetic disorder is minimized due to the frozen lattice vibrations. However, an important issue related to structural disorder of superlattices at low temperatures has received little attention to date. In this work, it is shown that CsPbBr3 nanocrystal superlattices undergo a reversible order-disorder transition upon cooling to 90 K. The transition consists of the loss of structural coherence, that is, increased nanocrystal misalignment, and contraction of the superlattices, as revealed by temperature-dependent X-ray diffraction, and is ascribed to the solidification of ligands (on the basis of Raman spectroscopy). Introducing shorter amines on the nanocrystal surface allows to mitigate these changes, improve order, and shorten interparticle distance. It is demonstrated that the low temperature phase of the short ligand-capped nanocrystal superlattices is characterized by a strong exciton migration observable in the photoluminescence decay, which is due to the shrinkage of the inter-nanocrystal distance.

Photo-Claisen Rearrangement in a Coumarin-Caged Peptide Leads to a Surprising Enzyme Hyperactivation

Protein phosphatase-1 (PP1) is a ubiquitous enzyme that counteracts hundreds of kinases in cells. PP1 interacts with regulatory proteins via an RVxF peptide motif that binds to a hydrophobic groove on the enzyme. PP1-disrupting peptides (PDPs) compete with these regulatory proteins, leading to the release of the active PP1 subunit and promoting substrate dephosphorylation. Building on previous strategies employing the ortho-nitrobenzyl (o-Nb) group as a photocage to control PDP activity, we introduced coumarin derivatives into a PDP via an ether bond to explore their effects on PP1 activity. Surprisingly, our study revealed that the coumarin-caged peptides (PDP-DEACM and PDP-CM) underwent a photo-Claisen rearrangement, resulting in an unexpected hyperactivation of PP1. Our findings underscore the importance of linker design in controlling uncaging efficiency of photocages and highlight the need for comprehensive in vitro analysis before cellular experiments.

Tracing the Chromatin: From 3C to Live-Cell Imaging

Chromatin organization plays a key role in gene regulation throughout the cell cycle. Understanding the dynamics governing the accessibility of chromatin is crucial for insight into mechanisms of gene regulation, DNA replication, and cell division. Extensive research has been done to track chromatin dynamics to explain how cells function and how diseases develop, in the hope of this knowledge leading to future therapeutics utilizing proteins or drugs that modify the accessibility or expression of disease-related genes. Traditional methods for studying the movement of chromatin throughout the cell relied on cross-linking spatially adjacent sections or hybridizing fluorescent probes to chromosomal loci and then constructing dynamic models from the static data collected at different time points. While these traditional methods are fruitful in understanding fundamental aspects of chromatin organization, they are limited by their invasive sample preparation protocols and diffraction-limited microscope resolution. These limitations have been challenged by modern methods based on high- or super-resolution microscopy and specific labeling techniques derived from gene targeting tools. These modern methods are more sensitive and less invasive than traditional methods, therefore allowing researchers to track chromosomal organization, compactness, and even the distance or rate of chromatin domain movement in detail and real time. This review highlights a selection of recently developed methods of chromatin tracking and their applications in fixed and live cells.

Phytoplankton cell-states: multiparameter fluorescence lifetime flow-based monitoring reveals cellular heterogeneity

Phytoplankton are a major source of primary productivity. Their photosynthetic fluorescence are unique measures of their type, physiological state, and response to environmental conditions. Changes in phytoplankton photophysiology are commonly monitored by bulk fluorescence spectroscopy, where gradual changes are reported in response to different perturbations, such as light intensity changes. What is the meaning of such trends in bulk parameters if their values report ensemble averages of multiple unsynchronized cells? To answer this, we developed an experimental scheme that enables tracking fluorescence intensities, brightnesses, and their ratios, as well as mean photon nanotimes equivalent to mean fluorescence lifetimes, one cell at a time. We monitored three different phytoplankton species during diurnal cycles and in response to an abrupt increase in light intensity. Our results show that we can define specific subpopulations of cells by their fluorescence parameters for each of the phytoplankton species, and in response to varying light conditions. Importantly, we identify the cells undergo well-defined transitions between these subpopulations. The approach shown in this work will be useful in the exact characterization of phytoplankton cell states and parameter signatures in response to different changes these cells experience in marine environments, which will be applicable for monitoring marine-related environmental effects.

Readily Accessible and Brightly Fluorogenic BODIPY/NBD-Tetrazines via SNAr Reactions

We describe SNAr reactions of some commercial amino-tetrazines and halo-dyes, which give efficiently quenched BODIPY/NBD-tetrazines (ΦFl < 0.01) in high yields and, importantly, with high purities affordable via simple silica gel chromatography only. The dyes exhibit large Stokes shifts, moderate environmental sensitivity, and emission enhancements (up to 193-fold) upon Tz ligation with BCN─a strained dienophile. They successfully serve as labels for HSA protein premodified with BCN, resulting in bright blue-green emission upon ligation.

Macrocyclic Dual-Locked "Turn-On" Drug for Selective and Traceless Release in Cancer Cells

Drug safety and efficacy due to premature release into the bloodstream and poor biodistribution remains a problem despite seminal advances in this area. To circumvent these limitations, we report drug cyclization based on dynamic covalent linkages to devise a dual lock for the small-molecule anticancer drug, camptothecin (CPT). Drug activity is "locked" within the cyclic structure by the redox responsive disulfide and pH-responsive boronic acid-salicylhydroxamate and turns on only in the presence of acidic pH, reactive oxygen species and glutathione through traceless release. Notably, the dual-responsive CPT is more active (100-fold) than the non-cleavable (permanently closed) analogue. We further include a bioorthogonal handle in the backbone for functionalization to generate cyclic-locked, cell-targeting peptide- and protein-CPTs, for targeted delivery of the drug and traceless release in triple negative metastatic breast cancer cells to inhibit cell growth at low nanomolar concentrations.

Chemical Reactions in Living Systems

The term "in vivo ("in the living") chemistry" refers to chemical reactions that take place in a complex living system such as cells, tissue, body liquids, or even in an entire organism. In contrast, reactions that occur generally outside living organisms in an artificial environment (e.g., in a test tube) are referred to as in vitro. Over the past decades, significant contributions have been made in this rapidly growing field of in vivo chemistry, but it is still not fully understood, which transformations proceed efficiently without the formation of by-products or how product formation in such complex environments can be characterized. Potential applications can be imagined that synthesize drug molecules directly within the cell or confer new cellular functions through controlled chemical transformations that will improve the understanding of living systems and develop new therapeutic strategies. The guiding principles of this contribution are twofold: 1) Which chemical reactions can be translated from the laboratory to the living system? 2) Which characterization methods are suitable for studying reactions and structure formation in complex living environments?

A ratiometric fluorescent probe based on the FRET platform for the detection of sulfur dioxide derivatives and viscosity

BACKGROUND

Sulfur dioxide (SO2) is a common gaseous pollutant that significantly threatens environmental pollution and human health. Meanwhile, viscosity is an essential parameter of the intracellular microenvironment, manipulating many physiological roles such as nutrient transport, metabolism, signaling regulation and apoptosis. Currently, most of the fluorescent probes used for detecting SO2 derivatives and viscosity are single-emission probes or probes based on the ICT mechanism, which suffer from short emission wavelengths, small Stokes shifts or susceptibility to environmental background. Therefore, the development of powerful high-performance probes for real-time monitoring of sulfur dioxide derivatives and viscosity is of great significance for human health.

RESULTS

In this research, we designed the fluorescent probe QQC to detect SO2 derivatives and viscosity based on FRET platform with quinolinium salt as donor and quinolinium-carbazole as acceptor. QQC exhibited a ratiometric fluorescence response to SO2 with a low detection limit (0.09 μM), large Stokes shift (186 nm) and high energy transfer efficiency (95 %), indicating that probe QQC had good sensitivity and specificity. In addition, QQC was sensitive to viscosity, with an 9.10-folds enhancement of orange fluorescence and an excellent linear relationship (R2 = 0.98) between the logarithm of fluorescence intensity at 592 nm and viscosity. Importantly, QQC could not only recognize SO2 derivatives in real water samples and food, but also detect viscosity changes caused by food thickeners and thereby had broad market application prospects.

SIGNIFICANCE

We have developed a ratiometric fluorescent probe based on the FRET platform for detecting sulfur dioxide derivatives and viscosity. QQC could not only successfully detect SO2 derivatives in food and water samples, but also be made into test strips for detecting HSO3-/SO32- solution. In addition, the probe was also used to detect viscosity changes caused by food thickeners. Therefore, this novel probe had significant value in food and environmental detection applications.

Photo- and X-ray Induced Cytotoxicity of CeF3-YF3-TbF3 Nanoparticle-Polyvinylpyrrolidone-"Radachlorin" Composites for Combined Photodynamic Therapy

The Ce0.5Y0.35Tb0.15F3 nanoparticles with a CeF3 hexagonal structure were synthesized using the co-precipitation technique. The average nanoparticle diameter was 14 ± 1 nm. The luminescence decay curves of the Ce0.5Y0.35Tb0.15F3 nanoparticles (λem = 541 nm, 5D4-7F5 transition of Tb3+) conjugated with Radachlorin using polyvinylpyrrolidone coating as well as without Radachlorin were detected. Efficient nonradiative energy transfer from Tb3+ to the Radachlorin was demonstrated. The maximum energy transfer coefficients for the nanoparticles conjugated with Radachlorin via polyvinylpyrrolidone and without the coating were 82% and 55%, respectively. The average distance between the nanoparticle surface and Radachlorin was R0 = 4.5 nm. The best results for X-ray-induced cytotoxicity were observed for the NP-PVP-Rch sample at the lowest Rch concentration. In particular, after X-ray irradiation, the survival of A549 human lung carcinoma cells decreased by ~12%.

Wide-field fluorescence lifetime imaging of neuron spiking and subthreshold activity in vivo

The development of voltage-sensitive fluorescent probes suggests fluorescence lifetime as a promising readout for electrical activity in biological systems. Existing approaches fail to achieve the speed and sensitivity required for voltage imaging in neuroscience applications. We demonstrated that wide-field electro-optic fluorescence lifetime imaging microscopy (EO-FLIM) allows lifetime imaging at kilohertz frame-acquisition rates, spatially resolving action potential propagation and subthreshold neural activity in live adult Drosophila. Lifetime resolutions of <5 picoseconds at 1 kilohertz were achieved for single-cell voltage recordings. Lifetime readout is limited by photon shot noise, and the method provides strong rejection of motion artifacts and technical noise sources. Recordings revealed local transmembrane depolarizations, two types of spikes with distinct fluorescence lifetimes, and phase locking of spikes to an external mechanical stimulus.

A Study on the Interactions of Proteinase K with Myricetin and Myricitrin by Multi-Spectroscopy and Molecular Modeling

Myricetin (MYR) and myricitrin (MYT) are well recognized for their nutraceutical value, such as antioxidant, hypoglycemic, and hypotensive effects. In this work, fluorescence spectroscopy and molecular modeling were adopted to investigate the conformational and stability changes of proteinase K (PK) in the presence of MYR and MYT. The experimental results showed that both MYR and MYT could quench fluorescence emission via a static quenching mechanism. Further investigation demonstrated that both hydrogen bonding and van der Waals forces play significant roles in the binding of complexes, which is consistent with the conclusions of molecular modeling. Synchronous fluorescence spectroscopy, Förster resonance energy transfer, and site-tagged competition experiments were performed to prove that the binding of MYR or MYT to PK could alter its micro-environment and conformation. Molecular docking results revealed that either MYR or MYT spontaneously interacted with PK at a single binding site via hydrogen bonding and hydrophobic interactions, which is consistent with the results of spectroscopic measurements. A 30 ns molecular dynamics simulation was conducted for both PK-MYR and PK-MYT complexes. The calculation results showed that no large structural distortions or interaction changes occurred during the entire simulation time span. The average RMSD changes of PK in PK-MYR and PK-MYT were 2.06 and 2.15 Å, respectively, indicating excellent stability of both complexes. The molecular simulation results suggested that both MYR and MYT could interact with PK spontaneously, which is in agreement with spectroscopic results. This agreement between experimental and theoretical results indicates that the method herein could be feasible and worthwhile for protein–ligand complex studies.

Fabrication of white light emitting diodes via high yield surface passivated carbon quantum dots doped with terbium

Exploiting the unique characteristics of various materials to create novel hybrid materials opens up innovative possibilities for cutting-edge applications across numerous fields. Here, we have synthesized novel surface functionalized photoluminescent carbon quantum dots (CQDs) doped with a rare-earth element (Tb³⁺) for white light emitting diodes. High quantum yield CQDs were produced utilizing Plumeria leaves as a precursor using a one-step hydrothermal approach, and further, its optical characterization was thoroughly investigated. Herein, the functionalized CQDs demonstrate excitation-independent electroluminescence performance. The UV-LED chip and functionalized CQD were combined to create a device that emits cold white light with Commission Internationale de L'Eclairage coordinates of (0.33, 0.34), a corresponding correlated color temperature of 4995 K and color rendering index of 84.2.

Cryogenic Fluorescence Spectroscopy of Ionic Fluorones in Gaseous and Condensed Phases: New Light on Their Intrinsic Photophysics

Fluorescence spectroscopy of gas-phase ions generated through electrospray ionization is an emerging technique able to probe intrinsic molecular photophysics directly without perturbations from solvent interactions. While there is ample scope for the ongoing development of gas-phase fluorescence techniques, the recent expansion into low-temperature operating conditions accesses a wealth of data on intrinsic fluorophore photophysics, offering enhanced spectral resolution compared with room-temperature measurements, without matrix effects hindering the excited-state dynamics. This perspective reviews current progress on understanding the photophysics of anionic fluorone dyes, which exhibit an unusually large Stokes shift in the gas phase, and discusses how comparison of gas- and condensed-phase fluorescence spectra can fingerprint structural dynamics. The capacity for temperature-dependent measurements of both fluorescence emission and excitation spectra helps establish the foundation for the use of fluorone dyes as fluorescent tags in macromolecular structure determination. We suggest ideas for technique development.

Elucidating the Oligomerization and Cellular Interactions of a Trimer Derived from Aβ through Fluorescence and Mass Spectrometric Studies

Aβ oligomers play a central role in the neurodegeneration observed with Alzheimer's disease. Our laboratory has developed covalently stabilized trimers derived from residues 17-36 of Aβ as model systems for studying Aβ oligomers. In the current study, we apply the emerging techniques of fluorescence lifetime imaging microscopy (FLIM) and native mass spectrometry (native MS) to better understand the assembly and interactions of the oligomer model system 2AT-L in aqueous solutions and with cells. 2AT-L and fluorescently labeled 2AT-L analogues assemble in the membrane-like environment of SDS-PAGE, showing diffuse bands of oligomers in equilibrium. Native ion mobility-mass spectrometry (native IM-MS) of 2AT-L allows for the identification of discrete oligomers in solution and shows similar patterns of oligomer formation between 2AT-L and fluorescently labeled analogues. Fluorescence microscopy with SH-SY5Y cells reveals that fluorescently labeled 2AT-L analogues colocalize within lysosomes. FLIM studies with phasor analysis further elucidate the assembly of 2AT-L within cells and establish the occurrence of FRET, indicating the presence of oligomers within cells. Collectively, these multiple complementary techniques help better understand the complex behavior of the 2AT-L model system.

A Critical Review on the Sensing, Control, and Manipulation of Single Molecules on Optofluidic Devices

Single-molecule techniques have shifted the paradigm of biological measurements from ensemble measurements to probing individual molecules and propelled a rapid revolution in related fields. Compared to ensemble measurements of biomolecules, single-molecule techniques provide a breadth of information with a high spatial and temporal resolution at the molecular level. Usually, optical and electrical methods are two commonly employed methods for probing single molecules, and some platforms even offer the integration of these two methods such as optofluidics. The recent spark in technological advancement and the tremendous leap in fabrication techniques, microfluidics, and integrated optofluidics are paving the way toward low cost, chip-scale, portable, and point-of-care diagnostic and single-molecule analysis tools. This review provides the fundamentals and overview of commonly employed single-molecule methods including optical methods, electrical methods, force-based methods, combinatorial integrated methods, etc. In most single-molecule experiments, the ability to manipulate and exercise precise control over individual molecules plays a vital role, which sometimes defines the capabilities and limits of the operation. This review discusses different manipulation techniques including sorting and trapping individual particles. An insight into the control of single molecules is provided that mainly discusses the recent development of electrical control over single molecules. Overall, this review is designed to provide the fundamentals and recent advancements in different single-molecule techniques and their applications, with a special focus on the detection, manipulation, and control of single molecules on chip-scale devices.

Fluorescence Resonance Energy Transfer Measurements in Polymer Science: A Review

Fluorescence resonance energy transfer (FRET) is a non-invasive characterization method for studying molecular structures and dynamics, providing high spatial resolution at nanometer scale. Over the past decades, FRET-based measurements are developed and widely implemented in synthetic polymer systems for understanding and detecting a variety of nanoscale phenomena, enabling significant advances in polymer science. In this review, the basic principles of fluorescence and FRET are briefly discussed. Several representative research areas are highlighted, where FRET spectroscopy and imaging can be employed to reveal polymer morphology and kinetics. These examples include understanding polymer micelle formation and stability, detecting guest molecule release from polymer host, characterizing supramolecular assembly, imaging composite interfaces, and determining polymer chain conformations and their diffusion kinetics. Finally, a perspective on the opportunities of FRET-based measurements is provided for further allowing their greater contributions in this exciting area.

The Rise and Future of Discrete Organic-Inorganic Hybrid Nanomaterials

Hybrid nanomaterials (HNs), the combination of organic semiconductor ligands attached to nanocrystal semiconductor quantum dots, have applications that span a range of practical fields, including biology, chemistry, medical imaging, and optoelectronics. Specifically, HNs operate as discrete, tunable systems that can perform prompt fluorescence, energy transfer, singlet fission, upconversion, and/or thermally activated delayed fluorescence. Interest in HNs has naturally grown over the years due to their tunability and broad spectrum of applications. This Review presents a brief introduction to the components of HNs, before expanding on the characterization and applications of HNs. Finally, the future of HN applications is discussed.

Electron-Hole Binding Governs Carrier Transport in Halide Perovskite Nanocrystal Thin Films

Two-dimensional halide perovskite nanoplatelets (NPLs) have exceptional light-emitting properties, including wide spectral tunability, ultrafast radiative decays, high quantum yields (QY), and oriented emission. Due to the high binding energies of electron-hole pairs, excitons are generally considered the dominant species responsible for carrier transfer in NPL films. To realize efficient devices, it is imperative to understand how exciton transport progresses therein. We employ spatially and temporally resolved optical microscopy to map exciton diffusion in perovskite nanocrystal (NC) thin films between 15 °C and 55 °C. At room temperature (RT), we find the diffusion length to be inversely correlated to the thickness of the nanocrystals (NCs). With increasing temperatures, exciton diffusion declines for all NC films, but at different rates. This leads to specific temperature turnover points, at which thinner NPLs exhibit higher diffusion lengths. We attribute this anomalous diffusion behavior to the coexistence of excitons and free electron hole-pairs inside the individual NCs within our temperature range. The organic ligand shell surrounding the NCs prevents charge transfer. Accordingly, any time an electron-hole pair spends in the unbound state reduces the FRET-mediated inter-NC transfer rates and, consequently, the overall diffusion. These results clarify how exciton diffusion progresses in strongly confined halide perovskite NC films, emphasizing critical considerations for optoelectronic devices.

Flow cytometry based-FRET: basics, novel developments and future perspectives

Förster resonance energy transfer (FRET) is a widespread technology used to analyze and quantify protein interactions in multiple settings. While FRET is traditionally measured by microscopy, flow cytometry based-FRET is becoming popular within the last decade and more commonly used. Flow cytometry based-FRET offers the possibility to assess FRET in a short time-frame in a high number of cells thereby allowing stringent and statistically robust quantification of FRET in multiple samples. Furthermore, established, simple and easy to implement gating strategies facilitate the adaptation of flow cytometry based-FRET measurements to most common flow cytometers. We here summarize the basics of flow cytometry based-FRET, highlight recent novel developments in this field and emphasize on exciting future perspectives.

Chromophoric Dendrimer-Based Materials: An Overview of Holistic-Integrated Molecular Systems for Fluorescence Resonance Energy Transfer (FRET) Phenomenon

Dendrimers (from the Greek dendros → tree; meros → part) are macromolecules with well-defined three-dimensional and tree-like structures. Remarkably, this hyperbranched architecture is one of the most ubiquitous, prolific, and recognizable natural patterns observed in nature. The rational design and the synthesis of highly functionalized architectures have been motivated by the need to mimic synthetic and natural-light-induced energy processes. Dendrimers offer an attractive material scaffold to generate innovative, technological, and functional materials because they provide a high amount of peripherally functional groups and void nanoreservoirs. Therefore, dendrimers emerge as excellent candidates since they can play a highly relevant role as unimolecular reactors at the nanoscale, acting as versatile and sophisticated entities. In particular, they can play a key role in the properties of light-energy harvesting and non-radiative energy transfer, allowing them to function as a whole unit. Remarkably, it is possible to promote the occurrence of the FRET phenomenon to concentrate the absorbed energy in photoactive centers. Finally, we think an in-depth understanding of this mechanism allows for diverse and prolific technological applications, such as imaging, biomedical therapy, and the conversion and storage of light energy, among others.

Recent progress on graphene quantum dots-based fluorescence sensors for food safety and quality assessment applications

The versatile photophysicalproperties, high surface-to-volume ratio, superior photostability, higher biocompatibility, and availability of active sites make graphene quantum dots (GQDs) an ideal candidate for applications in sensing, bioimaging, photocatalysis, energy storage, and flexible electronics. GQDs-based sensors involve luminescence sensors, electrochemical sensors, optical biosensors, electrochemical biosensors, and photoelectrochemical biosensors. Although plenty of sensing strategies have been developed using GQDs for biosensing and environmental applications, the use of GQDs-based fluorescence techniques remains unexplored or underutilized in the field of food science and technology. To the best of our knowledge, comprehensive review of the GQDs-based fluorescence sensing applications concerning food quality analysis has not yet been done. This review article focuses on the recent progress on the synthesis strategies, electronic properties, and fluorescence mechanisms of GQDs. The various GQDs-based fluorescence detection strategies involving Förster resonance energy transfer- or inner filter effect-driven fluorescence turn-on and turn-off response mechanisms toward trace-level detection of toxic metal ions, toxic adulterants, and banned chemical substances in foodstuffs are summarized. The challenges associated with the pretreatment steps of complex food matrices and prospects and challenges associated with the GQDs-based fluorescent probes are discussed. This review could serve as a precedent for further advancement in interdisciplinary research involving the development of versatile GQDs-based fluorescent probes toward food science and technology applications.

Unfolding Mechanisms and Conformational Stability of the Dimeric Endophilin N-BAR Domain

Endophilin, which is a member of the Bin-amphiphysin-Rvs (BAR) domain protein superfamily, contains a homodimeric N-BAR domain of a characteristic crescent shape. The N-BAR domain comprises a six-helix bundle and is known to sense and generate membrane curvature. Here, we characterize aspects of the unfolding mechanism of the endophilin A1 N-BAR domain during thermal denaturation and examine factors that influence the thermal stability of this domain. Far-UV circular dichroism (CD) spectroscopy was applied to monitor changes in the secondary structure above room temperature. The protein's conformational changes were further characterized through Foerster resonance energy transfer and cross-linking experiments at varying temperatures. Our results indicate that thermal unfolding of the endophilin N-BAR is (minimally) a two-step process, with a dimeric intermediate that displays partial helicity loss. Furthermore, a thermal shift assay and temperature-dependent CD were applied to compare the unfolding processes of several truncated versions of endophilin. The melting temperature of the N-BAR domain decreased when we deleted either the N-terminal H0 helix or the unstructured linker of endophilin. This result suggests that these intrinsically disordered domains may play a role in structurally stabilizing the functional N-BAR domain in vivo. Finally, we show that single-site mutations can also compromise endophilin's thermal stability.

Aggregation Induced Emissive Luminogens for Sensing of Toxic Elements

The major findings in the growing field of aggregation induced emissive (AIE) active materials for the detection of environmental toxic pollutants have been summarized and discussed in this Review article. Owing to the underlying photophysical phenomenon, fluorescent AIE active molecules show more impact on sensing applications. The major focus in current research efforts is on the development of AIE active materials such as TPE based organic fluorescent molecules, metal organic framework, and polymers that can be employed for the detection of toxic pollutants such as CN- , NO2- , Hg2+ , Cd2+ , As3+ , As5+ , F- , Pb2+ , Sb3+ ions.

Quo vadis FRET? Förster's method in the era of superresolution

Although the theoretical foundations of Förster resonance energy transfer (FRET) were laid in the 1940s as part of the quantum physical revolution of the 20th century, it was only in the 1970s that it made its way to biology as a result of the availability of suitable measuring and labeling technologies. Thanks to its ease of application, FRET became widely used for studying molecular associations on the nanometer scale. The development of superresolution techniques at the turn of the millennium promised an unprecedented insight into the structure and function of molecular complexes. Without downplaying the significance of superresolution microscopies this review expresses our view that FRET is still a legitimate tool in the armamentarium of biologists for studying molecular associations since it offers distinct advantages and overcomes certain limitations of superresolution approaches.

Time-resolved spectroscopy of radiative energy transfer between a conjugated oligomer and polymer in solution

We report a short investigation of the energy transfer process between the conjugated oligomer 1,4-bis(9-ethyl-3-carbazo-vinylene)-9,9-dihexyl-fluorene (BECV-DHF) and the conjugated polymer poly[2-methoxy-5-(3,7-dimethyloctyloxy)-1,4-phenylene-vinylene] - end capped with DMP (MDMO-PPV). The radiative energy transfer (RET) process shows a time delay, and the formation of the excimer causes a further delay. All these processes were studied using time-resolved spectroscopy (TRS), which has three-dimensional (3D) features with wavelength, intensity and time (picosecond) as the X, Y and Z-axis, respectively. We observed a definitive delay (1 ns) in the fluorescence from MEDMO-PPV concerning the fluorescence of the oligomer, indicating the RET. The TRS of different relative concentrations and temperature effects on the energy transfer process was also studied. The quantum yield, critical distance, polarizability and change of MEDMO-PPV were calculated. The excimer of the MEDMO-PPV produces Amplified Spontaneous Emission (ASE) after a time delay of at least 0.5 ns, which was also observed in this study.

Novel Imaging Modalities Shedding Light on Plant Biology: Start Small and Grow Big

The acquisition of quantitative information on plant development across a range of temporal and spatial scales is essential to understand the mechanisms of plant growth. Recent years have shown the emergence of imaging methodologies that enable the capture and analysis of plant growth, from the dynamics of molecules within cells to the measurement of morphometricand physiological traits in field-grown plants. In some instances, these imaging methods can be parallelized across multiple samples to increase throughput. When high throughput is combined with high temporal and spatial resolution, the resulting image-derived data sets could be combined with molecular large-scale data sets to enable unprecedented systems-level computational modeling. Such image-driven functional genomics studies may be expected to appear at an accelerating rate in the near future given the early success of the foundational efforts reviewed here. We present new imaging modalities and review how they have enabled a better understanding of plant growth from the microscopic to the macroscopic scale.

Recent advances in the synthesis and application of Yb-based fluoride upconversion nanoparticles

This review focuses on recent progress in the development of Yb-based upconversion nanoparticles and their emerging technological applications.

An invisible private 2D barcode design and implementation with tunable fluorescent nanoparticles

The popularity of 2D barcodes is playing a key role in simplifying people's daily life activities, such as identification, quick payment, checking in and checking out, etc. However, relevant issues have emerged as their popularity has soared. The most urgent and representative problem is decryption, which may lead to serious information leakage and substantial damage to organizations, such as governments and international enterprises. This issue is mainly due to the visibility of 2D barcodes. In order to prevent potential privacy violation and sensitive information leakage through easy access of those visible 2D barcodes, we have designed and fabricated invisible 2D barcodes that will only be visible under UV illumination. This approach provides a promising solution to address the previous problem by transferring 2D barcodes into an invisible state. We have employed a typical micro-emulsion method to fabricate polystyrene (PS) fluorescent nanoparticles due to its simplicity. The invisible patterns can and will only be accessed and recognized under UV light illumination to protect personal private information. These invisible 2D barcodes provide a feasible solution for personal information protection and fit with a patient's privacy protection scenario very well, as we have demonstrated.

Stacking among the clips of the poly-aromatic rings of phenazine with hydroxy-aromatics and photophysical properties

Clip-like arrangements of molecules in the cocrystals of phenazine with hydroxy-aromatics in their respective self-assemblies and photophysical properties were presented. Phenazine cocrystals with 1,2-dihydroxybenzene provided assembly with butterfly-like arrangements. In these cocrystals, the phenazine molecules occurred in parallel pairs having extensive π-stacking. The clip-like cocrystals with 1,3-dihydroxybenzene also exhibited parallel pairs of phenazine molecules that were parallel cofacial π-stacked. The hydrated cocrystals of phenazine with 1,2,3-trihydroxybenzene had chains of parallel cofacial phenazine rings having three distinguishable π-separation distances among the centroids of the phenazine rings. Also, 2,7-dihydroxynaphthalene formed a clip-like cocrystal with phenazine, which encapsulated an additional molecule of phenazine. This cocrystal also provided chain-like parallel arrangements of the phenazine molecules. The emission and quantum yields of the cocrystals were determined by the integrating sphere method, which indicated that only the cocrystal of phenazine with 2,7-dihydroxynaphthalene showed monomer-like emission of phenazine and the rest of the cocrystals were in a quenched state. In the solution phase, quenching of the emission of hydroxynaphthalene was observed when phenazine was added to an independent solution of 2,7-dihydroxynaphthalene or another hydroxynaphthalene. However, when hydroxybenzenes were added to a solution of phenazine, fluorescence enhancements of phenazine occurred due to photo-electron transfer.

π-Stackings control the photoluminescence efficiencies in solids, whereas in solutions, the ON or OFF processes are dependent on the hydroxyaromatics.

A Novel Conjugate of Bis[((4-bromophenyl)amino)quinazoline], a EGFR-TK Ligand, with a Fluorescent Ru(II)-Bipyridine Complex Exhibits Specific Subcellular Localization in Mitochondria

The epidermal growth factor receptor (EGFR) is a key target in anticancer research, whose aberrant function in malignancies has been linked to severe irregularities in critical cellular processes, including cell cycle progression, proliferation, differentiation, and survival. EGFR mutant variants, either transmembrane or translocated to the mitochondria and/or the nucleus, often exhibit resistance to EGFR inhibitors. The ability to noninvasively image and quantify EGFR provides novel approaches in the detection, monitoring, and treatment of EGFR-related malignancies. The current study aimed to deliver a new theranostic agent that combines fluorescence imaging properties with EGFR inhibition. This was achieved via conjugation of an in-house-developed ((4-bromophenyl)amino)quinazoline inhibitor of mutant EGFR-TK, selected from a focused aminoquinazoline library, with a [Ru(bipyridine)₃]²⁺ fluorophore. A triethyleneglycol-derived diamino linker featuring (+)-ionizable sites was employed to link the two functional moieties, affording two unprecedented Ru conjugates with 1:1 and 2:1 stoichiometry of aminoquinazoline to the Ru complex (mono-quinazoline-Ru-conjugate and bis-quinazoline-Ru-conjugate, respectively). The bis-quinazoline-Ru-conjugate, which retains an essential inhibitory activity, was found by fluorescence imaging to be effectively uptaken by Uppsala 87 malignant glioma (grade IV malignant glioma) cells. The fluorescence imaging study and a time-resolved fluorescence resonance energy transfer study indicated a specific subcellular distribution of the conjugate that coincides with that of a mitochondria-targeted dye, suggesting mitochondrial localization of the conjugate and potential association with mitochondria-translocated forms of EGFR. Mitochondrial localization was further documented by the specific concentration of the bis-quinazoline-Ru-conjugate in a mitochondrial isolation assay.

Plasmon-Enhanced Fluorescence Resonance Energy Transfer

In this review, we firstly introduce physical mechanism of fluorescence resonance energy transfer (FRET), the methods to measure FRET efficiency, and the applications of FRET. Secondly, we introduce the principle and applications of plasmon-enhanced fluorescence (PEF). Thirdly, we focused on the principle and applications of plasmon-enhanced FRET. This review can promote further understanding of FRET and PE-FRET.

Precision and accuracy of single-molecule FRET measurements-a multi-laboratory benchmark study

Single-molecule Förster resonance energy transfer (smFRET) is increasingly being used to determine distances, structures, and dynamics of biomolecules in vitro and in vivo. However, generalized protocols and FRET standards to ensure the reproducibility and accuracy of measurements of FRET efficiencies are currently lacking. Here we report the results of a comparative blind study in which 20 labs determined the FRET efficiencies (E) of several dye-labeled DNA duplexes. Using a unified, straightforward method, we obtained FRET efficiencies with s.d. between ±0.02 and ±0.05. We suggest experimental and computational procedures for converting FRET efficiencies into accurate distances, and discuss potential uncertainties in the experiment and the modeling. Our quantitative assessment of the reproducibility of intensity-based smFRET measurements and a unified correction procedure represents an important step toward the validation of distance networks, with the ultimate aim of achieving reliable structural models of biomolecular systems by smFRET-based hybrid methods.

A multi-laboratory study finds that single-molecule FRET is a reproducible and reliable approach for determining accurate distances in dye-labeled DNA duplexes.

Auto-FPFA: An Automated Microscope for Characterizing Genetically Encoded Biosensors

Genetically encoded biosensors function by linking structural change in a protein construct, typically tagged with one or more fluorescent proteins, to changes in a biological parameter of interest (such as calcium concentration, pH, phosphorylation-state, etc.). Typically, the structural change triggered by alterations in the bio-parameter is monitored as a change in either fluorescent intensity, or lifetime. Potentially, other photo-physical properties of fluorophores, such as fluorescence anisotropy, molecular brightness, concentration, and lateral and/or rotational diffusion could also be used. Furthermore, while it is likely that multiple photo-physical attributes of a biosensor might be altered as a function of the bio-parameter, standard measurements monitor only a single photo-physical trait. This limits how biosensors are designed, as well as the accuracy and interpretation of biosensor measurements. Here we describe the design and construction of an automated multimodal-microscope. This system can autonomously analyze 96 samples in a micro-titer dish and for each sample simultaneously measure intensity (photon count), fluorescence lifetime, time-resolved anisotropy, molecular brightness, lateral diffusion time, and concentration. We characterize the accuracy and precision of this instrument, and then demonstrate its utility by characterizing three types of genetically encoded calcium sensors as well as a negative control.

Axial Colocalization of Single Molecules with Nanometer Accuracy Using Metal-Induced Energy Transfer

Single-molecule localization based super-resolution microscopy has revolutionized optical microscopy and routinely allows for resolving structural details down to a few nanometers. However, there exists a rather large discrepancy between lateral and axial localization accuracy, the latter typically three to five times worse than the former. Here, we use single-molecule metal-induced energy transfer (smMIET) to localize single molecules along the optical axis, and to measure their axial distance with an accuracy of 5 nm. smMIET relies only on fluorescence lifetime measurements and does not require additional complex optical setups.