DCDHF Fluorophores for Single‐Molecule Imaging in Cells

There is a persistent need for small‐molecule fluorescent labels optimized for single‐molecule imaging in the cellular environment. Application of these labels comes with a set of strict requirements: strong absorption, efficient and stable emission, water solubility and membrane permeability, low background emission, and red‐shifted absorption to avoid cell autofluorescence. We have designed and characterized several fluorophores, termed “DCDHF” fluorophores, for use in live‐cell imaging based on the push–pull design: an amine donor group and a 2‐dicyanomethylene‐3‐cyano‐2,5‐dihydrofuran (DCDHF) acceptor group, separated by a π‐rich conjugated network. In general, the DCDHF fluorophores are comparatively photostable, sensitive to local environment, and their chemistries and photophysics are tunable to optimize absorption wavelength, membrane affinity, and solubility. Especially valuable are fluorophores with sophisticated photophysics for applications requiring additional facets of control, such as photoactivation. For example, we have reengineered a red‐emitting DCDHF fluorophore so that it is dark until photoactivated with a short burst of low‐intensity violet light. This molecule and its relatives provide a new class of bright photoactivatable small‐molecule fluorophores, which are needed for super‐resolution imaging schemes that require active control (here turning‐on) of single‐molecule emission.     

Single‐Molecule Localization Microscopy using mCherry

We demonstrate the potential of the commonly used red fluorescent protein mCherry for single‐molecule super‐resolution imaging. mCherry can be driven into a light‐induced dark state in the presence of a thiol from which it can recover spontaneously or by irradiation with near UV light. We show imaging of subcellular protein structures such as microtubules and the nuclear pore complex with a resolution below 40 nm. We were able to image the C‐terminus of the nuclear pore protein POM121, which is on the inside of the pore and not readily accessible for external labeling. The photon yield for mCherry is comparable to that of the latest optical highlighter fluorescent proteins. Our findings show that the widely used mCherry red fluorescent protein and the vast number of existing mCherry fusion proteins are readily amenable to super‐resolution imaging. This obviates the need for generating novel protein fusions that may compromise function or the need for external fluorescent labeling.     

Characterization of the photochromic pigments in red fluorescent proteins purified from the gut juice of the silkworm Bombyx mori L

Multiple forms of red fluorescent proteins (RFPs) were observed in the gut juice of the silkworm, Bombyx mori L. It is to be noted that only one RFP band is reported in the literature so far. However, we report here three electrophoretically separated RFPs (A, B and C) found to be heterogeneous with respect to their components, namely the protein part and the fluorescent tetrapyrrole pigment moiety. Of the three RFPs, band C was found to be a glycoprotein. The absorption extinction coefficients and fluorescence quantum yields of the three RFPs were estimated. Further, this is the first communication demonstrating the presence of three different chlorophyll derivatives associated with the three different RFPs. The pigments were analyzed by thin layer chromatography followed by their elution to characterize the pigments by spectrophotometric and spectrofluorometric methods. Spectral characteristics have led to the identification of monovinyl chlorophyllide a, divinyl protochlorophyllide a and monovinyl pheophytin a as being associated with RFP bands A, B and C, respectively. These three purified RFPs can serve as the source of the three pigments as the standards.     

Biohybrid fluorescent nanodiamonds as dual‐contrast markers for light and electron microscopies

Cathodoluminescence (CL) and correlative light‐electron microscopy (CLEM) are two useful analytical tools in diverse research areas. Recently, fluorescent nanodiamonds (FNDs) have emerged as promising imaging agents for both CL and CLEM owing to their exceptional photophysical and chemical properties. However, to realize their practical applications in the life sciences, surface modification and functionalization of the nanomaterials with bioactive molecules are critical and essential. Here we provide a comprehensive review on the methods of synthesizing biohybrid FNDs as well as recent advances of CL and CLEM imaging of cells with these carbon nanoparticles as dual‐contrast markers.     

Semiconducting polymer dots as near‐infrared fluorescent probes for bioimaging and sensing

In recent years, semiconducting polymer dots (Pdots) have emerged as a new type of ultrabright fluorescent probes, which have been proved to be very useful for biomedical imaging. Pdots possess several exceptional advantages including high fluorescence brightness, fast radiative rate, excellent photostability, and negligible cytotoxicity. Among these new types of Pdots, the near‐infrared (NIR) fluorescent Pdots appear to be the most urgent and important owing to their promising deep‐tissue imaging in the clinic. This mini‐review highlights the recent progress in the design of NIR‐emitting Pdots and their biomedical applications both in vitro and in vivo.     

Facile Microwave‐Assisted Solid‐Phase Synthesis of Highly Fluorescent Nitrogen–Sulfur‐Codoped Carbon Quantum Dots for Cellular Imaging Applications

Carbon quantum dots (CQDs) have recently attracted significant attention for both their fundamental science and technological applications as a new class of fluorescent zero‐dimensional nanomaterials with a size below 10 nm. However, the reported methods of synthesis were generally less suitable for the large‐scale production of the CQDs with high‐fluorescent quantum yield (QY). In the paper, a novel one‐pot microwave‐assisted drying synthesis approach was presented to prepare CQDs with high QY of 61.3 % for the first time. The production yield of CQDs was 35±3 % in weight. The as‐prepared CQDs were characterized by various techniques such as TEM, AFM, XRD, XPS, FTIR spectroscopy, UV/Vis absorption spectroscopy, and fluorescence spectroscopy. The results showed that the high QY of CQDs was largely attributed to the dual doping of nitrogen and sulphur into CQDs. Such CQDs were then used as live‐cell imaging reagents due to their high QY, good water dispersibility, fine biocompatibility, high photostability, and low cytotoxicity.     

Synthesis and Characterization of Far‐Red/NIR‐Fluorescent BODIPY Dyes,Solid‐State Fluorescence,and Application as Fluorescent Tags Attached to Carbon Nano‐onions

A series of π‐extended distyryl‐substituted boron dipyrromethene (BODIPY) derivatives with intense far‐red/near‐infrared (NIR) fluorescence was synthesized and characterized, with a view to enhance the dye’s performance for fluorescence labeling. An enhanced brightness was achieved by the introduction of two methyl substituents in the meso positions on the phenyl group of the BODIPY molecule; these substituents resulted in increased structural rigidity. Solid‐state fluorescence was observed for one of the distyryl‐substituted BODIPY derivatives. The introduction of a terminal bromo substituent allows for the subsequent immobilization of the BODIPY fluorophore on the surface of carbon nano‐onions (CNOs), which leads to potential imaging agents for biological and biomedical applications. The far‐red/NIR‐fluorescent CNO nanoparticles were characterized by absorption, fluorescence, and Raman spectroscopies, as well as by thermogravimetric analysis, dynamic light scattering, high‐resolution transmission electron microscopy, and confocal microscopy.     

A Far‐Red Emitting Fluorescent Chemogenetic Reporter for In Vivo Molecular Imaging

Far‐red emitting fluorescent labels are highly desirable for spectral multiplexing and deep tissue imaging. Here, we describe the generation of frFAST (far‐red Fluorescence Activating and absorption Shifting Tag), a 14‐kDa monomeric protein that forms a bright far‐red fluorescent assembly with (4‐hydroxy‐3‐methoxy‐phenyl)allylidene rhodanine (HPAR‐3OM). As HPAR‐3OM is essentially non‐fluorescent in solution and in cells, frFAST can be imaged with high contrast in presence of free HPAR‐3OM, which allowed the rapid and efficient imaging of frFAST fusions in live cells, zebrafish embryo/larvae, and chicken embryos. Beyond enabling the genetic encoding of far‐red fluorescence, frFAST allowed the design of a far‐red chemogenetic reporter of protein–protein interactions, demonstrating its great potential for the design of innovative far‐red emitting biosensors.     

Disassembly‐Driven Fluorescence Turn‐on of Polymerized Micelles by Reductive Stimuli in Living Cells

Stimuli‐response nanoparticles have emerged as powerful tools for imaging and therapeutic applications. Ideally, they should be assembled from biodegradable materials featuring small size and cooperative response to biological stimuli that trigger particle disassembly and release of an active molecule that could be readily monitored in situ. A concept is developed that consists of organic nanoparticles, assembled from fluorescent amphiphiles and polymerized with a redox‐cleavable cross‐linker. We obtained 20 nm nanoparticles bearing self‐quenched Nile Red dye residues, which can disassemble in living cells into highly fluorescent molecular units owing to an external or internal reductive stimulus. The obtained results pave the way to new stimuli‐responsive nanomaterials for applications in background‐free imaging as well as in drug delivery, as the concept can be further extended to other active molecules including drugs and to cross‐linkers cleavable by other biological stimuli.     

Far‐Red Organic Fluorophores Contain a Fluorescent Impurity

Far‐red organic fluorophores commonly used in traditional and super‐resolution localization microscopy are found to contain a fluorescent impurity with green excitation and near‐red emission. This near‐red fluorescent impurity can interfere with some multicolor stochastic optical reconstruction microscopy/photoactivated localization microscopy measurements in live cells and produce subtle artifacts in chemically fixed cells. We additionally describe alternatives to avoid artifacts in super‐resolution localization microscopy.     

Fluorescent protein barrel fluctuations and oxygen diffusion pathways in mCherry

Fluorescent proteins (FPs) are valuable tools as biochemical markers for studying cellular processes. Red fluorescent proteins (RFPs) are highly desirable for in vivo applications because they absorb and emit light in the red region of the spectrum where cellular autofluorescence is low. The naturally occurring fluorescent proteins with emission peaks in this region of the spectrum occur in dimeric or tetrameric forms. The development of mutant monomeric variants of RFPs has resulted in several novel FPs known as mFruits. Though oxygen is required for maturation of the chromophore, it is known that photobleaching of FPs is oxygen sensitive, and oxygen-free conditions result in improved photostabilities. Therefore, understanding oxygen diffusion pathways in FPs is important for both photostabilites and maturation of the chromophores. In this paper, we use molecular dynamics calculations to investigate the protein barrel fluctuations in mCherry, which is one of the most useful monomeric mFruit variant. We employ implicit ligand sampling to determine oxygen pathways from the bulk solvent into the mCherry chromophore in the interior of the protein. We also show that these pathways can be blocked or altered and barrel fluctuations can be reduced by strategic amino acid substitutions.     

Electronic excitations of green fluorescent proteins: modeling solvatochromatic shifts of red fluorescent protein chromophore model compound in aqueous solutions

While green fluorescent proteins (GFPs) have been widely used as tools in biochemistry, cell biology, and molecular genetics, novel red fluorescent proteins (RFPs) with red fluorescence emission have also been identified, as complements to the existing GFP technology. The unusual spectrophotometric and fluorescence properties of GFPs and RFPs are controlled by the protonation states and possibly cis/trans isomerization within their chromophores. In this work, we have investigated the electronic structures, liquid structures, and solvent shifts of the possible neutral and anionic protonated states and the cis/trans isomerization of a RFP chromophore model compound HBMPI in aqueous solutions. The calculations reproduced the experimental absorption solvatochromatic shifts of dilute HBMPI in water under neutral and anionic conditions. Unlike the GFP chromophore, the RFP chromophore model compound HBMPI in basic solution can only adopt a conformation where the C=C bond between the bridge group and the imidazolinone ring and the C-C bond between the imidazolinone and ethylene groups exist in cis and trans conformations, respectively. Moreover, the solvent-solute hydrogen-bonding interactions are found to contribute significantly to the total solvent shifts of pi-pi* excitations of aqueous HBMPI solutions, signifying the importance of protein environment in the determination of the conformation of the chromophores in red fluorescent proteins.     

Trans-cis isomerization is responsible for the red-shifted fluorescence in variants of the red fluorescent protein eqFP611

An important class of red fluorescent proteins (RFPs) feature a 2-iminomethyl-5-(4-hydroxybenzylidene)imidazolinone chromophore. Among these proteins, eqFP611 has the chromophore in a coplanar trans orientation, whereas the cis isomer is preferred by other RFPs such as DsRed and its variants. In the photoactivatable protein asFP595, the chromophore can even be switched from the nonfluorescent trans to the fluorescent cis state by light. By using X-ray crystallography, we have determined the structure of dimeric eqFP611 at high resolution (up to 1.1 A). In the far-red emitting eqFP611 variant d2RFP630, which carries an additional Asn143Ser mutation, the chromophore resides predominantly (approximately 80%) in the cis isomeric state, and in RFP639, which has Asn143Ser and Ser158Cys mutations, the chromophore is found completely in the cis form. The pronounced red shift of excitation and emission maxima of RFP639 can thus unambiguously be assigned to trans-cis isomerization of the chromophore. Among RFPs, eqFP611 is thus unique because its chromophore is highly fluorescent in both the cis and trans isomeric forms.     

Tracking the Dynamic Folding and Unfolding of RNA G‐Quadruplexes in Live Cells

Because of the absence of methods for tracking RNA G‐quadruplex dynamics, especially the folding and unfolding of this attractive structure in live cells, understanding of the biological roles of RNA G‐quadruplexes is so far limited. Herein, we report a new red‐emitting fluorescent probe, QUMA‐1 , for the selective, continuous, and real‐time visualization of RNA G‐quadruplexes in live cells. The applications of QUMA‐1 in several previously intractable applications, including live‐cell imaging of the dynamic folding, unfolding, and movement of RNA G‐quadruplexes and the visualization of the unwinding of RNA G‐quadruplexes by RNA helicase have been demonstrated. Notably, our real‐time results revealed the complexity of the dynamics of RNA G‐quadruplexes in live cells. We anticipate that the further application of QUMA‐1 in combination with appropriate biological and imaging methods to explore the dynamics of RNA G‐quadruplexes will uncover more information about the biological roles of RNA G‐quadruplexes.     

DNA Nanoflowers for Multiplexed Cellular Imaging and Traceable Targeted Drug Delivery

We present a facile approach to make aptamer‐conjugated FRET (fluorescent resonance energy transfer) nanoflowers (NFs) through rolling circle replication for multiplexed cellular imaging and traceable targeted drug delivery. The NFs can exhibit multi‐fluorescence emissions by a single‐wavelength excitation as a result of the DNA matrix covalently incorporated with three dye molecules able to perform FRET. Compared with the conventional DNA nanostructure assembly, NF assembly is independent of template sequences, avoiding the otherwise complicated design of DNA building blocks assembled into nanostructures by base‐pairing. The NFs were uniform and exhibited high fluorescence intensity and excellent photostability. Combined with the ability of traceable targeted drug delivery, these colorful DNA NFs provide a novel system for applications in multiplex fluorescent cellular imaging, effective screening of drugs, and therapeutic protocol development.     

A Small‐Molecule FRET Reporter for the Real‐Time Visualization of Cell‐Surface Proteolytic Enzyme Functions

Real‐time imaging of cell‐surface‐associated proteolytic enzymes is critical to better understand their performances in both physiological and pathological processes. However, most current approaches are limited by their complexity and poor membrane‐anchoring properties. Herein, we have designed and synthesized a unique small‐molecule fluorescent probe, which combines the principles of passive exogenous membrane insertion and Förster resonance energy transfer (FRET) to image cell‐surface‐localized furin‐like convertase activities. The membrane‐associated furin‐like enzymatic cleavage of the peptide probe leads to an increased fluorescence intensity which was mainly localized on the plasma membrane of the furin‐expressed cells. This small‐molecule fluorescent probe may serve as a unique and reliable reporter for real‐time visualization of endogenous cell‐surfaceassociated proteolytic furin‐like enzyme functions in live cells and tissues using one‐photon and two‐photon microscopy.     

Photoswitchable Fluorescent Nanoparticles: Preparation,Properties and Applications

This minireview highlights recent advances of research dedicated to photoswitchable fluorescent nanoparticles and their applications. Recently, several strategies have been developed to synthesize nanoparticles with optically switchable emission properties: either fluorescence on/off or dual‐alternating‐color fluorescence photoswitching. The underlying mechanisms of fluorescence photoswitching enable many different types of photoswitchable fluorescent nanoparticles to change fluorescence colors, thus validating the basis of the initial photoswitching design. Among all possible applications, the usage of photoswitchable fluorescent nanoparticles to empower super‐resolution fluorescence imaging and to label biological targets was subsequently reviewed. Finally, we summarize the important areas regarding future research and development on photoswitchable fluorescent nanoparticles.     

Fluorescent Protein Capped Mesoporous Nanoparticles for Intracellular Drug Delivery and Imaging

A multifunctional system for intracellular drug delivery and simultaneous fluorescent imaging was constructed by using histidine‐tagged, cyan fluorescent protein (CFP)‐capped magnetic mesoporous silica nanoparticles (MMSNs). This protein‐capped multifunctional nanostructure is highly biocompatible and does not affect cell viability or proliferation. The CFP acts not only as a capping agent, but also as a fluorescent imaging agent. The nanoassembly was activated by histidine‐based replacement, leading to release of drug molecules encapsulated in the nanopores into the bulk solution. The fluorescent imaging functionality would allow noninvasive tracking of the nanoparticles in the body. By combining the drug delivery with cell‐imaging capability, these nanoparticles may provide valuable multifunctional nanoplatforms for biomedical applications.     

Photoelectrocyclization as an Activation Mechanism for Organelle‐Specific Live‐Cell Imaging Probes

Photoactivatable fluorophores are useful tools in live‐cell imaging owing to their potential for precise spatial and temporal control. In this report, a new photoactivatable organelle‐specific live‐cell imaging probe based on a 6π electrocyclization/oxidation mechanism is described. It is shown that this new probe is water‐soluble, non‐cytotoxic, cell‐permeable, and useful for mitochondrial imaging. The probe displays large Stokes shifts in both pre‐activated and activated forms, allowing simultaneous use with common dyes and fluorescent proteins. Sequential single‐cell activation experiments in dense cellular environments demonstrate high spatial precision and utility in single‐ or multi‐cell labeling experiments.