Single-molecule redox blinking of perylene diimide derivatives in water

In Operando Visualization of Elementary Turnovers in Photocatalytic Organic Synthesis

We report the in operando visualization of the photocatalytic turnovers on single eosin Y (EY) through a redox-induced photoblinking phenomenon. The photocatalytic cyclization of thiobenzamide (TB) catalyzed by EY was investigated. The analysis of the intensity-versus-time trajectories of single EYs revealed the kinetics and dynamics of the elementary photocatalytic turnovers and the heterogeneity of the activity of individual EYs. The quenching turnover time showed a fast population and a slow population, which could be attributed to the singlet and triplet states of photoexcited EY. The slow quenching turnovers were more dominant at higher TB concentrations. The activity heterogeneity of EYs was studied over a series of reactant concentrations. Excess quenching reagent was found to decrease the percentage of active EYs. The method can be broadly applied to studying the elementary processes of photocatalytic organic reactions in operando.

Symmetry-Breaking Charge Separation in a Chiral Bis(perylenediimide) Probed at Ensemble and Single-Molecule Levels

Chiral molecular assemblies exhibiting symmetry-breaking charge separation (SB-CS) are potential candidates for the development of chiral organic semiconductors. Herein, we explore the excited-state dynamics of a helically chiral perylenediimide bichromophore (Cy-PDI2) exhibiting SB-CS at the ensemble and single-molecule levels. Solvent polarity-tunable interchromophoric excitonic coupling in chiral Cy-PDI2 facilitates the interplay of SB-CS and excimer formation in the ensemble domain. Analogous to the excited-state dynamics of Cy-PDI2 at the ensemble level, single-molecule fluorescence lifetime traces of Cy-PDI2 depicted long-lived off-states characteristic of the radical ion pair-mediated dark states. The discrete electron transfer and charge separation dynamics in Cy-PDI2 at the single-molecule level are governed by the distinct influence of the local environment. The present study aims at understanding the fundamental excited-state dynamics in chiral organic bichromophores for designing efficient chiral organic semiconductors and applications toward charge transport materials.

Pulse Radiolysis Investigation of Radicals Derived from Water-Soluble Cyanine Dyes: Implications for Super-resolution Microscopy

Light-induced blinking, an inherent feature of many forms of super-resolution microscopy, has been linked to transient reduction of the fluorescent cyanine dye used as an imaging agent. There is, however, only scant literature information related to one-electron reduced cyanine dyes, especially in an aqueous environment. Here, we examine a small series of cyanine dyes, possessing disparate π-conjugation lengths, under selective reducing or oxidizing conditions. The experiment allows recording of both differential absorption spectra and decay kinetics of the resultant one-electron reduced or oxidized transient species in water. Relative to the ground state, absorption transitions for the various radicals are weak and somewhat broadened but do allow correlation with the π-conjugation length. In all cases, absorption maxima lie to the blue of the main ground-state transition. Under anaerobic conditions, the transient species decay on the microsecond to millisecond time scale, with the mean lifetime depending on molecular structure, radiation dose, and dye concentration. The experimental absorption spectra recorded for the one-electron reduced radicals and the presumed dimer cation radical compare well to spectra obtained from time-dependent density functional theory calculations. The results allow conclusions to be drawn regarding the plausibility of the reduced species being responsible for light-induced blinking in direct stochastic optical reconstruction microscopy.

Ultrasmall, Bright, and Photostable Fluorescent Core-Shell Aluminosilicate Nanoparticles for Live-Cell Optical Super-Resolution Microscopy

Stochastic optical reconstruction microscopy (STORM) is an optical super-resolution microscopy (SRM) technique that traditionally requires toxic and non-physiological imaging buffers and setups that are not conducive to live-cell studies. It is observed that ultrasmall (<10 nm) fluorescent core-shell aluminosilicate nanoparticles (aC' dots) covalently encapsulating organic fluorophores enable STORM with a single excitation source and in a regular (non-toxic) imaging buffer. It is shown that fourfold coordinated aluminum is responsible for dye blinking, likely via photoinduced redox processes. It is demonstrated that this phenomenon is observed across different dye families leading to probes brighter and more photostable than the parent free dyes. Functionalization of aC' dots with antibodies allows targeted fixed cell STORM imaging. Finally, aC' dots enable live-cell STORM imaging providing quantitative measures of the size of intracellular vesicles and the number of particles per vesicle. The results suggest the emergence of a powerful ultrasmall, bright, and photostable optical SRM particle platform with characteristics relevant to clinical translation for the quantitative assessment of cellular structures and processes from live-cell imaging.

Physical insights into protection effect of conjugated polymers by natural antioxidants

Conjugated polymers (CPs) known as organic semiconductors have been broadly applied in photovoltaic and light emitting devices due to their easy fabrication and flexibility. However, one of the bottlenecks limiting the application of CPs is their poor photostability upon continuous excitation which is one of the crucial parameters of CPs. How to improve the photostability of CPs is always one of the key questions in this field. In this work, we found that the photostability of poly(3-hexylthiophene-2,5-diyl) (P3HT) molecules can be largely improved by addition of vitamin E (VE) in bulk solution, solid films and single molecules. In solution and films, VE can not only significantly retard the photodegradation of P3HT but also enhance the fluorescence intensity. For individual P3HT molecules, with increasing VE concentrations, the on-time duration increases and the off-time duration becomes shorter. VE as natural antioxidants can not only donate electrons to the long-lived charged species but also quench the triplet states of CPs via energy transfer accelerating the depopulation process back to the ground state. The short duration time of the charged species and the triplet states provides higher fluorescence intensity. Furthermore, VE can also directly react with singlet oxygen or other reactive oxygen species (ROS) preventing them from reacting with CPs. These results not only provide an efficient strategy for improving the photostability of conjugated polymers in solution and films, but also shed light on better understanding the photophysics of conjugated polymers at single-molecule level.

Synthesis of unsymmetric perylenediimide dye molecule and its photochemical properties on lipid membrane

Optical manipulation of cellular function is one of the important targets in chemical biology and medicine. To achieve manipulation of cellular function using small molecules, photochemical reaction, such as photo-isomerization and photo-induced electron transfer, is one of the most promising reactions. Especially, photo-induced electron transfer process may be the crucial for their further development of photo-functional agents in living cells. However, such molecules, which enable the modification of cellular function, are limited and the further development is necessary. Herein, we synthesized a novel unsymmetric perylenediimide dye and investigated the cellular staining upon the addition in the cell culture medium. Furthermore, we observed the fluorescence quenching upon the addition of ascorbic acid as electron donor and report the preliminary results to manipulate Ca²⁺ concentration in living cell line upon 488-nm light photoirradiation.

Amphiphilic DNA Organic Hybrids: Functional Materials in Nanoscience and Potential Application in Biomedicine

Due to the addressability and programmability, DNA has been applied not merely in constructing static elegant nanostructures such as two dimensional and three dimensional DNA nanostructures but also in designing dynamic nanodevices. Moreover, DNA could combine with hydrophobic organic molecules to be a new amphiphilic building block and then self-assemble into nanomaterials. Of particular note, a recent state-of-the-art research has turned our attention to the amphiphilic DNA organic hybrids including small molecule modified DNA (lipid-DNA, fluorescent molecule-DNA, etc.), DNA block copolymers, and DNA-dendron hybrids. This review focuses mainly on the development of their self-assembly behavior and their potential application in nanomaterial and biomedicine. The potential challenges regarding of the amphiphilic DNA organic hybrids are also briefly discussed, aiming to advance their practical applications in nanoscience and biomedicine.

A solution-based single-molecule study of surface-bound PBIs: solvent-mediated environmental effects on molecular flexibility

We have investigated the fundamental photophysical properties of surface-bound perylene bisimide (PBI) molecules in solution at the single-molecule level.

A simple and versatile design concept for fluorophore derivatives with intramolecular photostabilization

Intramolecular photostabilization via triple-state quenching was recently revived as a tool to impart synthetic organic fluorophores with 'self-healing' properties. To date, utilization of such fluorophore derivatives is rare due to their elaborate multi-step synthesis. Here we present a general strategy to covalently link a synthetic organic fluorophore simultaneously to a photostabilizer and biomolecular target via unnatural amino acids. The modular approach uses commercially available starting materials and simple chemical transformations. The resulting photostabilizer-dye conjugates are based on rhodamines, carbopyronines and cyanines with excellent photophysical properties, that is, high photostability and minimal signal fluctuations. Their versatile use is demonstrated by single-step labelling of DNA, antibodies and proteins, as well as applications in single-molecule and super-resolution fluorescence microscopy. We are convinced that the presented scaffolding strategy and the improved characteristics of the conjugates in applications will trigger the broader use of intramolecular photostabilization and help to emerge this approach as a new gold standard.

Cell membrane permeable fluorescent perylene bisimide derivatives for cell lysosome imaging

The cellular uptake of Lyso-APBIprobes is improved by PEG chains, and the double morpholine moieties make Lyso-APBI probes have higher acid activation ratio and better cell lysosome specificity.

Fluorescent PET probes based on perylene-3,4,9,10-tetracarboxylic tetraesters

We demonstrate that perylene tetraester-based fluorescent PET probes with aniline receptors attached at the bay-positions are superior pH-sensitive “light-up” probes, with high fluorescence quantum yields Φ_F and huge fluorescent enhancements.

Sequential superresolution imaging of multiple targets using a single fluorophore

Fluorescence superresolution (SR) microscopy, or fluorescence nanoscopy, provides nanometer scale detail of cellular structures and allows for imaging of biological processes at the molecular level. Specific SR imaging methods, such as localization-based imaging, rely on stochastic transitions between on (fluorescent) and off (dark) states of fluorophores. Imaging multiple cellular structures using multi-color imaging is complicated and limited by the differing properties of various organic dyes including their fluorescent state duty cycle, photons per switching event, number of fluorescent cycles before irreversible photobleaching, and overall sensitivity to buffer conditions. In addition, multiple color imaging requires consideration of multiple optical paths or chromatic aberration that can lead to differential aberrations that are important at the nanometer scale. Here, we report a method for sequential labeling and imaging that allows for SR imaging of multiple targets using a single fluorophore with negligible cross-talk between images. Using brightfield image correlation to register and overlay multiple image acquisitions with ~10 nm overlay precision in the x-y imaging plane, we have exploited the optimal properties of AlexaFluor647 for dSTORM to image four distinct cellular proteins. We also visualize the changes in co-localization of the epidermal growth factor (EGF) receptor and clathrin upon EGF addition that are consistent with clathrin-mediated endocytosis. These results are the first to demonstrate sequential SR (s-SR) imaging using direct stochastic reconstruction microscopy (dSTORM), and this method for sequential imaging can be applied to any superresolution technique.

Perylene-cored star-shaped polycations for fluorescent gene vectors and bioimaging

Two star polycations, poly(2-aminoethyl methacrylate) (PAEMA, P1) and poly(2-(dimethylamino)ethyl methacrylate) (PDMAEMA, P2), have been synthesized with perylene diimide (PDI) as the central fluorophore. (1)H NMR and (13)C NMR are used to confirm the successful synthesis of a macromolecular initiator. Using ATRP strategy, P1 and P2 are obtained with narrow molecular weight distribution. The star polymers have good fluorescence properties in aqueous solution, which provides fluorescent tracing and imaging during gene delivery. Both P1 and P2 can efficiently condense DNA into stable nanoparticles. Transfection studies demonstrate that P1 and P2 deliver DNA into live cells with higher efficiency and lower cytotoxicity than polyethylenimine (PEI, 25 kDa). P2 shows higher capacity for gene delivery than P1 due to its better buffering and faster rate of cellular internalization.

Alternating-laser excitation: single-molecule FRET and beyond

The alternating-laser excitation (ALEX) scheme continues to expand the possibilities of fluorescence-based assays to study biological entities and interactions. Especially the combination of ALEX and single-molecule Förster Resonance Energy Transfer (smFRET) has been very successful as ALEX enables the sorting of fluorescently labelled species based on the number and type of fluorophores present. ALEX also provides a convenient way of accessing the correction factors necessary for determining accurate molecular distances. Here, we provide a comprehensive overview of the concept and current applications of ALEX and we explicitly discuss how to obtain fully corrected distance information across the entire FRET range. We also present new ideas for applications of ALEX which will push the limits of smFRET-based experiments in terms of temporal and spatial resolution for the study of complex biological systems.

Opportunities and challenges in single-molecule and single-particle fluorescence microscopy for mechanistic studies of chemical reactions

In recent years, single-molecule and single-particle fluorescence microscopy has emerged as a tool to investigate chemical systems. After an initial lag of over a decade with respect to biophysical studies, this powerful imaging technique is now revealing mechanisms of 'classical' organic reactions, spatial distribution of chemical reactivity on surfaces and the phase of active catalysts. The recent advance into commercial imaging systems obviates the need for home-built laser systems and thus opens this technique to traditionally trained synthetic chemists. We discuss the requisite photophysical and chemical properties of fluorescent reporters and highlight the main challenges in applying single-molecule techniques to chemical questions. The goal of this Perspective is to provide a snapshot of an emerging multidisciplinary field and to encourage broader use of this young experimental approach that aids the observation of chemical reactions as depicted in many textbooks: molecule by molecule.

Mechanism of intramolecular photostabilization in self-healing cyanine fluorophores

Organic fluorophores, which are popular labels for microscopy applications, intrinsically suffer from transient and irreversible excursions to dark-states. An alternative to adding photostabilizers at high concentrations to the imaging buffer relies on the direct linkage to the fluorophore. However, the working principles of this approach are not yet fully understood. In this contribution, we investigate the mechanism of intramolecular photostabilization in self-healing cyanines, in which photodamage is automatically repaired. Experimental evidence is provided to demonstrate that a single photostabilizer, that is, the vitamin E derivative Trolox, efficiently heals the cyanine fluorophore Cy5 in the absence of any photostabilizers in solution. A plausible mechanism is that Trolox interacts with the fluorophore through intramolecular quenching of triplet-related dark-states, which is a mechanism that appears to be common for both triplet-state quenchers (cyclooctatetraene) and redox-active compounds (Trolox, ascorbic acid, methylviologen). Additionally, the influence of solution-additives, such as cysteamine and procatechuic acid, on the self-healing process are studied. The results suggest the potential applicability of self-healing fluorophores in stochastic optical reconstruction microscopy (STORM) with optical super-resolution. The presented data contributes to an improved understanding of the mechanism involved in intramolecular photostabilization and has high relevance for the future development of self-healing fluorophores, including their applications in various research fields.

Long-wavelength, photostable, two-photon excitable BODIPY fluorophores readily modifiable for molecular probes

Near-infrared (NIR) fluorescent probes are increasingly popular in biological imaging and sensing, as long-wavelength (650-900 nm) excitation and emission have the advantages of minimum photodamage, deep tissue penetration, and minimum interference from autofluorescence in living systems. Here, a series of long-wavelength BODIPY dyes SPC, DC-SPC, DPC, and DC-DPC are synthesized conveniently and efficiently. They exhibit excellent photophysical properties in far red to near-infrared region, including large extinction coefficients, high fluorescence quantum yields, good photostability, and reasonable two-photon absorption cross section. Comparison of single-molecular imaging confirms that DPC is a much more efficient and more photostable NIR fluorophore than the commonly used Cy5. Also importantly, two kinds of convenient functionalization sites have been reserved: the aryl iodide for organometallic couplings and the terminal alkyne groups for click reactions. Further derivatives DC-SPC-PPh3 exhibit specificity to localize in mitochondria. The introduction of triphenylphosphonium (TPP) moieties mediates its hydrophilic-lipophilic balance and makes DC-SPC-PPh3 appropriate for cell labeling. Their long-wavelength emission at ∼650 nm can efficiently avoid the spectral crosstalk with other probes emitting in the visible light region. Superior photostability, low cytotoxicity, and two-photon excitable properties demonstrate its utility as a standard colocalizing agent to estimate the other probes' local distribution.

Polyglycerol-Dendronized Perylenediimides as Stable, Water-Soluble Fluorophores

The synthesis and photophysical properties of water-soluble, fluorescent polyglycerol-dendronized perylenediimides 1-4 are reported. The polyglycerol dendrons, which are known to be highly biocompatible, are found to confer high water-solubility on the perylenediimide in aqueous media while retaining its excellent fluorescent properties. Furthermore, intramolecular cross-linking of the polyglycerol dendrons using the ring-closing metathesis reaction not only enhances the photostability but also reduces the size of perylenediimide-cored dendrimers. The permeability of the various dendritic shells is probed using heavy metal ion quenchers and compared to non-dendritic but water-soluble perylenediimide 5.

Modification of n-type organic semiconductor performance of perylene diimides by substitution in different positions: two-dimensional π-stacking and hydrogen bonding

Perylene diimides (PDIs) and their derivatives are active n-type semiconducting materials widely used in organic electronic devices. A series of PDI derivatives have been investigated by quantum chemistry calculations combined with Marcus-Hush electron-transfer theory. The substitution of three different sites of a PDI induces large changes in its electron-transfer mobility. 2,5,8,11-Tetrachloro-PDI with four chlorine atoms in ortho positions shows both large electron- and hole-transfer mobilities of 0.116 and 0.650 cm(2) V(-1) s(-1) , respectively, indicative of a potentially highly efficient ambipolar organic semiconducting material. The calculated electron-transfer mobility of 1,6,7,12-tetrachloro-PDI is 0.081 cm(2) V(-1) s(-1) , which is in good agreement with the experimental result. Octachloro-PDIs have the largest electron mobility among these derivatives, although the π system of the central core is twisted. 2D π-stacking and hydrogen bonds formed at the imide positions are responsible for the large mobility. Simulated anisotropic transport mobility curves of these materials prove the magnitude of the mobility that appears when the measuring transistor channel is along the a-axis of the crystal, which is the direction of hydrogen bond formation.

Ortho-functionalized perylenediimides for highly fluorescent water-soluble dyes

Clearly visible: A water-soluble and highly fluorescent perylenediimide is synthesized via ruthenium-catalyzed alkylation with outstanding yields. For the first time, the possibility to use phosphonate derivatives in a Murai-type reaction is demonstrated.

Linking single-molecule blinking to chromophore structure and redox potentials

Intensity fluctuations between an ON-state and an OFF-state, also called blinking, are common to all luminescent objects when studied at the level of individuals. We studied blinking of three dyes from a homologous series (Cy3, Cy5, Cy7). The underlying radical anion states were induced by removing oxidants (i.e. oxygen) and by adding the reductant ascorbic acid. We find that for different conditions with distinct levels of oxidants in solution the OFF-state lifetime always increases in the order Cy3<Cy5<Cy7. Longer OFF-times are related to higher reduction potentials of the fluorophores, which increase with the size of the chromophore. Interestingly, we find reaction rates of the radical anion that are unexpectedly low at the assumed oxygen concentration. On the other hand, reaction rates meet the expectations of similar Rehm-Weller plots when methylviologen is used as oxidant, confirming the model of photoinduced reduction and oxidation reactions. The relation of OFF-state lifetimes to redox potentials might enable predictions about the nature of dark states, depending on the fluorophores' nano-environment in super-resolution microscopy.

Monovalent, clickable, uncharged, water-soluble perylenediimide-cored dendrimers for target-specific fluorescent biolabeling

Herein we report the synthesis of water-soluble polyglycerol-dendronized perylenediimides with a single reactive group that undergoes high-yielding click reactions. Single-molecule studies and target-specific biolabeling are reported, including the highly specific labeling of proteins on the surface of living bacterial and mammalian cells.

PALM and STORM: unlocking live-cell super-resolution

Live-cell fluorescence light microscopy has emerged as an important tool in the study of cellular biology. The development of fluorescent markers in parallel with super-resolution imaging systems has pushed light microscopy into the realm of molecular visualization at the nanometer scale. Resolutions previously only attained with electron microscopes are now within the grasp of light microscopes. However, until recently, live-cell imaging approaches have eluded super-resolution microscopy, hampering it from reaching its full potential for revealing the dynamic interactions in biology occurring at the single molecule level. Here we examine recent advances in the super-resolution imaging of living cells by reviewing recent breakthroughs in single molecule localization microscopy methods such as PALM and STORM to achieve this important goal.

Cyanine dyes in biophysical research: the photophysics of polymethine fluorescent dyes in biomolecular environments

The breakthroughs in single molecule spectroscopy of the last decade and the recent advances in super resolution microscopy have boosted the popularity of cyanine dyes in biophysical research. These applications have motivated the investigation of the reactions and relaxation processes that cyanines undergo in their electronically excited states. Studies show that the triplet state is a key intermediate in the photochemical reactions that limit the photostability of cyanine dyes. The removal of oxygen greatly reduces photobleaching, but induces rapid intensity fluctuations (blinking). The existence of non-fluorescent states lasting from milliseconds to seconds was early identified as a limitation in single-molecule spectroscopy and a potential source of artifacts. Recent studies demonstrate that a combination of oxidizing and reducing agents is the most efficient way of guaranteeing that the ground state is recovered rapidly and efficiently. Thiol-containing reducing agents have been identified as the source of long-lived dark states in some cyanines that can be photochemically switched back to the emissive state. The mechanism of this process is the reversible addition of the thiol-containing compound to a double bond in the polymethine chain resulting in a non-fluorescent molecule. This process can be reverted by irradiation at shorter wavelengths. Another mechanism that leads to non-fluorescent states in cyanine dyes is cis–trans isomerization from the singlet-excited state. This process, which competes with fluorescence, involves the rotation of one-half of the molecule with respect to the other with an efficiency that depends strongly on steric effects. The efficiency of fluorescence of most cyanine dyes has been shown to depend dramatically on their molecular environment within the biomolecule. For example, the fluorescence quantum yield of Cy3 linked covalently to DNA depends on the type of linkage used for attachment, DNA sequence and secondary structure. Cyanines linked to the DNA termini have been shown to be mostly stacked at the end of the helix, while cyanines linked to the DNA internally are believed to partially bind to the minor or major grooves. These interactions not only affect the photophysical properties of the probes but also create a large uncertainty in their orientation.