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Hundreds of proteins interact with poly(ADP-ribose) (PAR) via multiple PAR interaction motifs, thereby regulating their physico-chemical properties, sub-cellular localizations, enzymatic activities, or protein stability. Here, we present a targeted approach based on fluorescence correlation spectroscopy (FCS) to characterize potential structure-specific interactions of PAR molecules of defined chain length and branching with three prime PAR-binding proteins, the tumor suppressor protein p53, histone H1, and the histone chaperone APLF. Our study reveals complex and structure-specific PAR–protein interactions. Quantitative Kd values were determined and binding affinities for all three proteins were shown to be in the nanomolar range. We report PAR chain length dependent binding of p53 and H1, yet chain length independent binding of APLF. For all three PAR binders, we found a preference for linear over hyperbranched PAR. Importantly, protein- and PAR-structure-specific binding modes were revealed. Thus, while the H1-PAR interaction occurred largely on a bi-molecular 1:1 basis, p53—and potentially also APLF—can form complex multivalent PAR–protein structures. In conclusion, our study gives detailed and quantitative insight into PAR–protein interactions in a solution-based setting at near physiological buffer conditions. The results support the notion of protein and PAR-structure-specific binding modes that have evolved to fit the purpose of the respective biochemical functions and biological contexts.

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Although single-particle level studies on prolate ellipsoidal colloids are relatively abundant, similar studies on oblate ellipsoids are rare because suitable model systems are scarcely available. Here, we present the preparation of monodisperse hard core–shell oblate ellipsoids that can be imaged and tracked in 3D with confocal laser scanning microscopy. Using a thermomechanical squeezing method, we transform spherical core–shell polymethyl-methacrylate (PMMA) particles into oblate ellipsoids. We show how the shape polydispersity as well as the aspect ratio of the obtained oblate ellipsoids can be controlled. In addition, we discuss how the core–shell geometry limits the range of aspect ratios because of the different viscoelastic properties of the cross-linked PMMA core and linear PMMA shell. We further demonstrate imaging of the core–shell oblate dispersions on a single-particle level in real space and time and the tracking of position and orientation using our recently developed tracking algorithm for anisotropic core–shell colloids. Our results thus provide the tools for the future investigation of the behavior of oblate ellipsoids, especially in dense suspensions.

Cephalopod mollusks are endowed with an impressive range of features that have captured the attention of scientists from different fields, the imaginations of artists, and the interests of the public. The ability to spontaneously regrow lost or damaged structures quickly and functionally is among one of the most notable peculiarities that cephalopods possess. Microscopical imaging techniques represent useful tools for investigating the regenerative processes in several species, from invertebrates to mammals. However, these techniques have had limited use in cephalopods mainly due to the paucity of specific and commercially available markers. In addition, the commonly used immunohistochemical staining methods provide data that are specific to the antigens studied. New microscopical methods were recently applied to vertebrates to investigate regenerative events. Among them, multiphoton microscopy appears promising. For instance, it does not depend on species-related epitopes, taking advantage of the specific characteristics of tissues and allowing for its use in a species-independent way. Here, we illustrate the results obtained by applying this label-free imaging technique to the injured arm of

The hydrolysis of nucleotides is of paramount importance as an energy source for cellular processes. In addition, the transfer of phosphates from nucleotides onto proteins is important as a post-translational protein modification. Monitoring the enzymatic turnover of nucleotides therefore offers great potential as a tool to follow enzymatic activity. While a number of fluorescence sensors are known, so far, there are no methods available for the real-time monitoring of ATP hydrolysis inside live cells. We present the synthesis and application of a novel fluorogenic adenosine 5'-tetraphosphate (Ap4) analog suited for this task. Upon enzymatic hydrolysis, the molecule displays an increase in fluorescence intensity, which provides a readout of its turnover. We demonstrate how this can be used for monitoring cellular processes involving Ap4 hydrolysis. To this end, we visualized the enzymatic activity in live cells using confocal fluorescence microscopy of the Ap4 analog. Our results demonstrate that the Ap4 analog is hydrolyzed in lysosomes. We show that this approach is suited to visualize the lysosome distribution profiles within the live cell and discuss how it can be employed to gather information regarding autophagic flux. ispartof: INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES vol:22 issue:16 ispartof: location:Switzerland status: published

In the quest to decipher the chain of life from molecules to cells, the biological and biophysical questions being asked increasingly demand techniques that are capable of identifying specific biomolecules in their native environment, and can measure biomolecular interactions quantitatively, at the smallest possible scale in space and time, without perturbing the system under observation. The interaction of light with biomolecules offers a wealth of phenomena and tools that can be exploited to drive this progress. This Roadmap is written collectively by prominent researchers and encompasses selected aspects of bio-nano-photonics, spanning from the development of optical micro/nano-spectroscopy technologies for quantitative bioimaging and biosensing to the fundamental understanding of light–matter interaction phenomena with biomolecules at the nanoscale. It will be of interest to a wide cross-disciplinary audience in the physical sciences and life sciences.

Significance Using tailor-made colloids and confocal microscopy, we study the effect of shape on the glass transition in 3D suspensions of ellipsoidal colloids. Experimental data, supporting simulations, and a theoretical analysis reveal a unique state: liquid glass. In liquid glasses, orientational degrees of freedom are frozen whereas translation is free. Global nematic order is absent. We show that, in the liquid glass state, nematic precursors as hitherto unknown structures exist. In these, nematic order is suppressed by the intersection of clusters of ordered particles with differently ordered particles. Our data thus give insight into the glass transition and reveal an additional state of matter. The latter is expected to also have implications in liquid crystal formation., Despite the omnipresence of colloidal suspensions, little is known about the influence of colloid shape on phase transformations, especially in nonequilibrium. To date, real-space imaging results at high concentrations have been limited to systems composed of spherical colloids. In most natural and technical systems, however, particles are nonspherical, and their structural dynamics are determined by translational and rotational degrees of freedom. Using confocal microscopy of fluorescently labeled core–shell particles, we reveal that suspensions of ellipsoidal colloids form an unexpected state of matter, a liquid glass in which rotations are frozen while translations remain fluid. Image analysis unveils hitherto unknown nematic precursors as characteristic structural elements of this state. The mutual obstruction of these ramified clusters prevents liquid crystalline order. Our results give insight into the interplay between local structures and phase transformations. This helps to guide applications such as self-assembly of colloidal superstructures and also gives evidence of the importance of shape on the glass transition in general.

Simple and robust assays to monitor enzymatic ATP cleavage with high efficiency in real‐time are scarce. To address this shortcoming, we developed fluorescently labelled adenosine tri‐, tetra‐ and pentaphosphate analogues of ATP. The novel ATP analogues bear — in contrast to earlier reports — only a single acridone‐based dye at the terminal phosphate group. The dye's fluorescence is quenched by the adenine component of the ATP analogue and is restored upon cleavage of the phosphate chain and dissociation of the dye from the adenosine moiety. Thereby the activity of ATP‐cleaving enzymes can be followed in real‐time. We demonstrate this proficiency for ubiquitin activation by the ubiquitin‐activating enzymes UBA1 and UBA6 which represents the first step in an enzymatic cascade leading to the covalent attachment of ubiquitin to substrate proteins, a process that is highly conserved from yeast to humans. We found that the efficiency to serve as cofactor for UBA1/UBA6 very much depends on the length of the phosphate chain of the ATP analogue: triphosphates are used poorly while pentaphosphates are most efficiently processed. Notably, the novel pentaphosphate‐harbouring ATP analogue supersedes the efficiency of recently reported dual‐dye labelled analogues and thus, is a promising candidate for broad applications., Novel fluorescently labelled ATP analogues for direct monitoring of ubiquitin activation: Fluorescently modified adenosine tri‐, tetra‐ and pentaphosphates (ATP) analogues changing their fluorescence properties upon enzymatic turnover have been synthesised and applied to both E1s found in humans. Pentaphosphates were found to have superior processing and with the used acridone fluorophore the read‐out showed both fluorescence intensity and lifetime, making this assay versatile in application.

Adenosine triphosphate (ATP) probes modified with fluorescence dyes that change their fluorescence properties upon cleavage are an interesting tool for monitoring enzymatic ATP turnover. As a readout parameter, fluorescence lifetime is attractive because it is nearly independent of concentration. In our study, we synthesised and investigated fifteen different ATP analogues, in which the fluorophores were attached to the γ-phosphate of ATP. All analogues showed distinctly different fluorescence lifetimes compared to the corresponding values of the free fluorophores. Both increases and decreases in fluorescence lifetime were observed upon attachment to ATP. To shed light on the photophysical processes governing the lifetime changes, we performed photoelectron spectroscopy in air (PESA) to determine HOMO energy levels and time-resolved fluorescence spectroscopy to obtain rate constants. We present evidence that fluorescence quenching in the compounds tested is dynamic and attributed to photoinduced electron transfer (PET), whereas fluorescence lifetime increases are caused by stacking interactions between chromophore and the nucleobase reducing non-radiative relaxation. Finally, we demonstrate that enzymatic cleavage of the ATP analogues presented can be followed by continuous monitoring of fluorescence lifetime changes. published

Water-soluble, fluorescence-switchable derivatives of pyrrolopyrrole cyanines (PPCys) which serve as near-infrared pH indicators have been synthesized. The dyes reported have pKa values of 2.4–3.4 and thus are suitable for sensing in highly acidic environments. The new pH probes were evaluated by fluorescence imaging experiments in a cellular environment

Summary Nonlinear optical techniques which provide vibrational contrast have gained increasing attention in microscopy during the last two decades. After outlining the potential of these techniques, we give a brief introduction to coherent anti-Stokes Raman scattering, stimulated Raman scattering and sum frequency generation and discuss their suitability for contrast generation in optical microscopy. The rapid developments in these fields during the last decade have resulted in many different applications. Three exemplary application areas will therefore be presented in the last part of this manuscript.

Colloidal polymer particles are an important class of materials finding use in both everyday and basic research applications. Tailoring their composition, shape, and functionality is of key importance. In this article, we describe a new class of shape-tunable core-shell microparticles. They are composed of a cross-linked polystyrene (PS) core and a poly(methyl methacrylate) (PMMA) shell of varying thickness. In the first step, we prepared highly cross-linked PS cores, which are subsequently transferred into a nonpolar dispersant. They serve as the seed dispersion for a nonaqueous dispersion polymerization to generate the PMMA shell. The shape of the particles can subsequently be manipulated. After the shell growth stage, the spherical PS/PMMA core-shell colloids exhibit an uneven and wrinkled surface. An additional tempering procedure allows for smoothing the surface of the core-shell colloids. This results in polymer core-shell particles with a perfectly spherical shape. In addition to this thermal smoothing of the PMMA shell, we generated a selection of shape-anisotropic core-shell particles using a thermomechanical stretching procedure. Because of the unique constitution, we can selectively interrogate molecular vibrations in the PS core or the PMMA shell of the colloids using nonlinear optical microscopy techniques. This is of great interest because no photobleaching occurs, such that the particles can be tracked in real space over long times.

During the adipogenic differentiation process of mesenchymal stem cells, lipid droplets (LDs) grow slowly by transferring lipids between each other. Recent findings hint at the possibility that a fusion pore is involved. In this study, we analyze lipid transfer data obtained in long-term label-free microscopy studies in the framework of a Hagen-Poiseuille model. The data obtained show a LD fusion process in which the lipid transfer directionality depends on the size difference between LDs, whereas the respective rates depend on the size difference and additionally on the diameter of the smaller LDs. For the data analysis, the viscosity of the transferred material has to be known. We demonstrate that a viscosity-dependent molecular rotor dye can be used to measure LD viscosities in live cells. On this basis, we calculate the diameter of a putative lipid transfer channel which appears to have a direct dependence on the diameter of the smaller of the two participating LDs.

Electroporation is a physical method of transferring molecules into cells and tissues. It takes advantage of the transient permeabilization of the cell membrane induced by electric field pulses, which gives hydrophilic molecules access to the cytoplasm. This method offers high transfer efficiency for small molecules that freely diffuse through electrically permeabilized membranes. Larger molecules, such as plasmid DNA, face several barriers (plasma membrane, cytoplasmic crowding, and nuclear envelope), which reduce transfection efficiency and engender a complex mechanism of transfer. Our work provides insight into the way electrotransferred DNA crosses the cytoplasm to reach the nucleus. For this purpose, single-particle tracking experiments of fluorescently labeled DNA were performed. Investigations were focused on the involvement of the cytoskeleton using drugs disrupting or stabilizing actin and tubulin filaments as the two relevant cellular networks for particle transport. The analysis of 315 movies (~4,000 trajectories) reveals that DNA is actively transported through the cytoskeleton. The large number of events allows a statistical quantification of the DNA motion kinetics inside the cell. Disruption of both filament types reduces occurrence and velocities of active transport and displacements of DNA particles. Interestingly, stabilization of both networks does not enhance DNA transport.

Carcinoembryonic antigen-related cell adhesion molecule 3 (CEACAM3) is a phagocytic receptor on human granulocytes, which mediates the opsonin-independent recognition and internalization of a restricted set of Gram-negative bacteria such as Neisseria gonorrhoeae. In an unbiased screen using a SH2 domain microarray we identified the SH2 domain of growth factor receptor-bound protein 14 (Grb14) as a novel binding partner of CEACAM3. Biochemical assays and microscopic studies demonstrated that the Grb14 SH2 domain promoted the rapid recruitment of this adaptor protein to the immunoreceptor-based activation motif (ITAM)-like sequence within the cytoplasmic domain of CEACAM3. Furthermore, FRET-FLIM analyses confirmed the direct association of Grb14 and CEACAM3 in intact cells at the sites of bacteria-host cell contact. Knockdown of endogenous Grb14 by RNA interference as well as Grb14 overexpression indicate an inhibitory role for this adapter protein in CEACAM3-mediated phagocytosis. Therefore, Grb14 is the first negative regulator of CEACAM3-initiated bacterial phagocytosis and might help to focus granulocyte responses to the subcellular sites of pathogen-host cell contact. CAPSULE: BACKGROUND: CEACAM3-mediated phagocytosis is an innate mechanism to eliminate CEACAM-binding pathogenic bacteria. RESULTS: Biochemical analyses and FRET-FLIM imaging reveal the direct binding of the adaptor protein Grb14 to the tyrosine-phosphorylated cytoplasmic domain of CEACAM3, and this interaction limits phagocytosis. CONCLUSION: Grb14 is a negative regulator of CEACAM3-mediated phagocytosis. SIGNIFICANCE: Deciphering CEACAM3 interaction partners illuminates the minimal set of cellular factors controlling phagocytosis.

A highly stable setup for stimulated Raman scattering (SRS) microscopy is presented. It is based on a two-branch femtosecond Er:fiber laser operating at a 40 MHz repetition rate. One of the outputs is directly modulated at the Nyquist frequency with an integrated electro-optic modulator (EOM). This compact source combines a jitter-free pulse synchronization with a broad tunability and allows for shot-noise limited SRS detection. The performance of the SRS microscope is illustrated with measurements on samples from material science and cell biology. published

Gene electrotransfer is a powerful method of DNA delivery offering several medical applications, among the most promising of which are DNA vaccination and gene therapy for cancer treatment. Electroporation entails the application of electric fields to cells which then experience a local and transient change of membrane permeability. Although gene electrotransfer has been extensively studied in in vitro and in vivo environments, the mechanisms by which DNA enters and navigates through cells are not fully understood. Here we present a comprehensive review of the body of knowledge concerning gene electrotransfer that has been accumulated over the last three decades. For that purpose, after briefly reviewing the medical applications that gene electrotransfer can provide, we outline membrane electropermeabilization, a key process for the delivery of DNA and smaller molecules. Since gene electrotransfer is a multipart process, we proceed our review in describing step by step our current understanding, with particular emphasis on DNA internalization and intracellular trafficking. Finally, we turn our attention to in vivo testing and methodology for gene electrotransfer.

Poly(ADP-ribos)ylation (PARylation) is an important posttranslational protein modification, and is involved in major cellular processes such as gene regulation and DNA repair. Its dysregulation has been linked to several diseases, including cancer. Despite its importance, methods to observe PARylation dynamics within cells are rare. By following a chemical biology approach, we developed a fluorescent NAD(+) analogue that proved to be a competitive building block for protein PARylation in vitro and in cells. This allowed us to directly monitor the turnover of PAR in living cells at DNA damage sites after near-infrared (NIR) microirradiation. Additionally, covalent and noncovalent interactions of selected target proteins with PAR chains were visualized in cells by using FLIM-FRET microscopy. Our results open up new opportunities for the study of protein PARylation in real time and in live cells, and will thus contribute to a better understanding of its significance in a cellular context. published

Poly(ADP‐Ribos)ylierung (PARylierung) ist eine wichtige posttranslationale Proteinmodifikation, die in grundlegende zelluläre Prozesse wie Genregulation und DNA‐Reparatur involviert ist. Ihre Fehlregulierung wurde mit verschiedenen Krankheiten wie Krebs in Verbindung gebracht. Trotz größter Wichtigkeit gibt es nur wenige Methoden, um PARylierung und ihre Dynamik in Zellen zu beobachten. Mittels einer chemisch‐biologischen Herangehensweise entwickelten wir ein fluoreszierendes NAD+‐Analogon, das sich als kompetitiver Baustein für die PARylierung von Proteinen in vitro und in Zellen erwies. Dies ermöglichte uns, den Umsatz von PAR direkt und in lebenden Zellen nach DNA‐Schädigung durch NIR‐Mikrobestrahlung zu verfolgen. Zusätzlich wurden mithilfe von FLIM‐FRET‐Mikroskopie kovalente und nichtkovalente Interaktionen von PAR mit ausgewählten Proteinen sichtbar gemacht. Unsere Ergebnisse eröffnen neue Chancen für die schnelle zelluläre Untersuchung der Protein‐PARylierung in Echtzeit und werden somit zu einem besseren Verständnis und höherer Aussagekraft im zellulären Kontext beitragen. published

Poly(ADP-ribos)ylation (PARylation) is a major posttranslational modification and signaling event in most eukaryotes. Fundamental processes like DNA repair and transcription are coordinated by this transient polymer and its binding to proteins. ADP-ribosyltransferases (ARTs) build complex ADP-ribose chains from NAD+ onto various acceptor proteins. Molecular studies of PARylation thus remain challenging. Herein, we present the development of bioorthogonally functionalized NAD+ analogues for the imaging of PARylation in vitro and in cells. Our results show that 2-modified NAD+ analogues perform remarkably well and can be applied to the in-cell visualization of PARylation simultaneously in two colors. This tool gives insight into the substrate scope of ARTs and will help to further elucidate the biological role of PARylation by offering fast optical, multichannel read-outs. published

Background: Micro-lipid droplets (mLDs) appear in adipocytes upon lipolytic stimulation. LDs may grow by spontaneous, homotypic fusion. Results: Scavenging of fatty acids prevents mLD formation. LDs grow by a slow transfer of lipids between LDs. Conclusion: mLDs form due to fatty acid overflow. LD growth is a controlled process. Significance: Novel mechanistic insights into LD remodeling are provided., Synthesis, storage, and turnover of triacylglycerols (TAGs) in adipocytes are critical cellular processes to maintain lipid and energy homeostasis in mammals. TAGs are stored in metabolically highly dynamic lipid droplets (LDs), which are believed to undergo fragmentation and fusion under lipolytic and lipogenic conditions, respectively. Time lapse fluorescence microscopy showed that stimulation of lipolysis in 3T3-L1 adipocytes causes progressive shrinkage and almost complete degradation of all cellular LDs but without any detectable fragmentation into micro-LDs (mLDs). However, mLDs were rapidly formed after induction of lipolysis in the absence of BSA in the culture medium that acts as a fatty acid scavenger. Moreover, mLD formation was blocked by the acyl-CoA synthetase inhibitor triacsin C, implicating that mLDs are synthesized de novo in response to cellular fatty acid overload. Using label-free coherent anti-Stokes Raman scattering microscopy, we demonstrate that LDs grow by transfer of lipids from one organelle to another. Notably, this lipid transfer between closely associated LDs is not a rapid and spontaneous process but rather occurs over several h and does not appear to require physical interaction over large LD surface areas. These data indicate that LD growth is a highly regulated process leading to the heterogeneous LD size distribution within and between individual cells. Our findings suggest that lipolysis and lipogenesis occur in parallel in a cell to prevent cellular fatty acid overflow. Furthermore, we propose that formation of large LDs requires a yet uncharacterized protein machinery mediating LD interaction and lipid transfer.

DNA electrotransfer is a successful technique for gene delivery into cells and represents an attractive alternative to virus-based methods for clinical applications including gene therapy and DNA vaccination. However, little is currently known about the mechanisms governing DNA internalization and its fate inside cells. The objectives of this work were to investigate the role of endocytosis and to quantify the contribution of different routes of cellular trafficking during DNA electrotransfer. To pursue these objectives, we performed flow cytometry and single-particle fluorescence microscopy experiments using inhibitors of endocytosis and endosomal markers. Our results show that similar to 50% of DNA is internalized by caveolin/raft-mediated endocytosis, 25% by clathrin-mediated endocytosis, and 25% by macropinocytosis. During active transport, DNA is routed through multiple endosomal compartments with, in the hour following electrotransfer, 70% found in Rab5 structures, 50% in Rab11-containing organelles and 30% in Rab9 compartments. Later, 60% of DNA colocalizes with Lamp1 vesicles. Because these molecular markers can overlap while following organelles through several steps of trafficking, the percentages do not sum up to 100%. We conclude that electrotransferred DNA uses the classical endosomal trafficking pathways. Our results are important for a generalized understanding of gene electrotransfer, which is crucial for its safe use in clinics.

New applications have recently led to an increased interest in near infrared (NIR) dyes. Both, strong NIR absorption and fluorescence emission are important phenomena. While fluorescence is exploited especially for labelling purposes in microscopy, NIR absorption has a broad range of applications mainly in material science. Examples of growing fields of interest are NIR light emitting diodes and the use of NIR-photosensitizers in dye-sensitized solar cells. In the latter cases, the aim is to utilize the NIR part of the solar spectrum in order to generate photocurrents. In many applications, especially selective NIR absorbers which absorb strongly in the NIR while exhibiting negligible absorption in the visible spectral range are required. Dyes with these properties find use as NIR absorbers in paints and windows to block off heat, in laser protecting glasses, as dyes for laser polymer welding of transparent components, or as anti-forgery markers. In all these examples it is required that the dye does not influence the spectral properties of the components in the visible. Thus, photostable dyes with strong, narrowbandwidth NIR absorptions and negligible absorption in the visible spectral range are needed. Common strategies to achieve bathochromic shifts of the absorption maximum of a dye are the extension of the chromophoric system or the introduction of donor and acceptor groups into the chromophore. Cyanine dyes and the rylene dyes are the most popular classes showing significant bathochromic shifts upon extension of their π-system. In cyanine dyes, however, the chemical stability decreases with increasing extension. By contrast, rylene dyes are chemically very stable, but, due to comparably large bondlength changes accompanying the S0→S1 transition, they show rather intense 01 and 02 vibronic bands (Franck-Condon principle). Thus, their S0→S1 absorption is extended into the visible range. Other important classes of NIR dyes, showing strong and narrowband NIR absorption are squarine dyes, bodipys and some aza[18]annulene derivatives such as porphyrins phthalocyanines and especially naphtolocyanines. We recently described pyrrolopyrrole cyanine (PPCy) dyes as a new class of NIR dyes and fluorophores. PPCys are synthesized by a condensation reaction of diketopyrrolopyrrole (DPP) 1 and heteroaromatic acetonitriles (HAA) 3. Complexation with either BF2 or BPh2 yields fluorophores which exhibit narrowband absorption between 650 and 900 nm and fluorescence emission with high quantum yields. By isolation of the monoactivated DPP 2, selectivly one of the carbonyl groups of the DPP can be reacted with a HAA 3 to the half converted products 4. Further reaction with another acetonitrile derivative 3 leads to PPCys with an asymmetric substitution pattern. This stepwise reaction scheme allows for the introduction of just one functional group. Here, we describe the synthesis of a new class of NIR chromophores with unprecedented spectral properties. They have very strong and narrowband NIR absorption while featuring negligible visible absorption. The absorption coefficients of these dyes in the NIR belong to the strongest ever reported for organic fluorophores, being twice as high as those of recently reported rylene dyes. Our previous approaches to shift the absorption of the PPCys bathochromically concerned the modification of the heteroaromatic endgroup (A) and/or the complexation agent. The selective synthesis of the halfconverted DPPs 4 opens a strategy to enlarge the chromophore of the PPCys by reacting two equivalents of 4 with a bifunctional bridging heteroaromatic acetonitrile such as 5 (Scheme 1.) The resulting condensation products contain two pyrrolopyrrole moieties and can therefore be called bis-pyrrolopyrrole cyanine dyes.

The contrast mechanisms used for photoacoustic tomography (PAT) and fluorescence imaging differ in subtle, but significant, ways. The design of contrast agents for each or both modalities requires an understanding of the spectral characteristics as well as intra- and intermolecular interactions that occur during formulation. We found that fluorescence quenching that occurs in the formulation of near-infrared (NIR) fluorescent dyes in nanoparticles results in enhanced contrast for PAT. The ability of the new PAT method to utilize strongly absorbing chromophores for signal generation allowed us to convert a highly fluorescent dye into an exceptionally high PA contrast material. Spectroscopic characterization of the developed NIR dye-loaded perfluorocarbon-based nanoparticles for combined fluorescence and PA imaging revealed distinct dye-dependent photophysical behavior. We demonstrate that the enhanced contrast allows detection of regional lymph nodes of rats in vivo with time-domain optical and photoacoustic imaging methods. The results further show that the use of fluorescence lifetime imaging, which is less dependent on fluorescence intensity, provides a strategic approach to bridge the disparate contrast reporting mechanisms of fluorescence and PA imaging methods.

Nonlinear optical endoscopy is an attractive technique for biomedical imaging since it promises to give access to high resolution imaging in vivo. Among the various techniques used for endoscopic contrast generation, coherent anti-Stokes Raman scattering (CARS) is especially interesting. CARS endoscopy allows molecule specific imaging of unlabeled samples. In this contribution, we describe the design, implementation, and experimental characterization of a rigid, compact CARS endoscope with a spatial resolution of 750 nm over a field of view of roughly 250 μm. Omission of the relay optics and use of a gradient index lens specifically designed for this application allow one to realize these specifications in an endoscopic unit which is 2.2 mm wide over a length of 187 mm, making clinical applications during surgical interventions possible. Multimodal use of the endoscope is demonstrated with images of samples with neurosurgical relevance.

Sonogashira coupling of dibromo- and diethynyl-substituted benzenes and fluorenes in aqueous mini-emulsion afforded colloidally stable dispersions of highly fluorescent 60-120 nm particles of poly(arylene ethynylene)s of molecular weights M(n) 4 × 10(4)-2 × 10(5) g mol(-1) with solids contents up to 15 wt %. By covalent incorporation of diethynyl pyrrolo-pyrrole or diethynyl fluorenone in the mini-emulsion polymerization the emission color of these photostable nanoparticles can be tuned from blue (λ(em max) 470) to orange at a given excitation wavelength due to an efficient energy transfer to these acceptors. Two-photon action cross sections of the particles amount to 10(6) to 10(7) GM. The particles from emulsion polymerization are taken up by HeLa cells without an adverse effect on the cells. Differentiation of the location in cells of particle species varying in emission color was demonstrated for both linear and two-photon excitation microscopy in the NIR regime.

Diffusional changes during the radical bulk polymerization of styrene with and without crosslinker were investigated. Full correlation fluorescence correlation spectroscopy (fcFCS) allowed for the simultaneous detection of rotational and translational diffusion of single fluorescent perylene diimide probes. Small probes show a parallel decrease of both motions whereas for larger probes translation slows down faster than rotation. The latter behavior contradicts the relationship between the Stokes-Einstein and the Stokes-Einstein-Debye equation and is attributed to changes in the microviscosity and mesh size effects of the synthesized polymer chains. The introduction of permanent cross-links results in additional restrictions for translational diffusion whereas rotation is not significantly affected up to high monomer-to-polymer conversions.

Stimulated Raman scattering (SRS) microscopy is an important non-linear optical technique for the investigation of unlabeled samples. The SRS signal manifests itself as a small intensity exchange between the laser pulses involved in coherent excitation of Raman modes. Usually, high-frequency modulation is applied in one pulse train, and the signal is then detected on the other pulse train via lock-in amplification. While allowing shot-noise limited detection sensitivity, lock-in detection, which corresponds to filtering the signal in the frequency domain, is not the most efficient way of using the excitation light. In this manuscript, we show that boxcar averaging, which is equivalent to temporal filtering, is better suited for the detection of low-duty-cycle signals as encountered in SRS microscopy. We demonstrate that by employing suitable gating windows, the signal-to-noise ratios achievable with lock-in detection can be realized in shorter time with boxcar averaging. Therefore, high-quality images are recorded at a faster rate and lower irradiance which is an important factor, e.g., for minimizing degradation of biological samples.Stimulated Raman scattering (SRS) microscopy is an important non-linear optical technique for the investigation of unlabeled samples. The SRS signal manifests itself as a small intensity exchange between the laser pulses involved in coherent excitation of Raman modes. Usually, high-frequency modulation is applied in one pulse train, and the signal is then detected on the other pulse train via lock-in amplification. While allowing shot-noise limited detection sensitivity, lock-in detection, which corresponds to filtering the signal in the frequency domain, is not the most efficient way of using the excitation light. In this manuscript, we show that boxcar averaging, which is equivalent to temporal filtering, is better suited for the detection of low-duty-cycle signals as encountered in SRS microscopy. We demonstrate that by employing suitable gating windows, the signal-to-noise ratios achievable with lock-in detection can be realized in shorter time with boxcar averaging. Therefore, high-quality images are...

Single molecule spectroscopy experiments are reported for native peridinin–chlorophyll a–protein (PCP) complexes, and three reconstituted light-harvesting systems, where an N-terminal construct of native PCP from Amphidinium carterae has been reconstituted with chlorophyll (Chl) mixtures: with Chl a, with Chl b and with both Chl a and Chl b. Using laser excitation into peridinin (Per) absorption band we take advantage of sub-picosecond energy transfer from Per to Chl that is order of magnitude faster than the Forster energy transfer between the Chl molecules to independently populate each Chl in the complex. The results indicate that reconstituted PCP complexes contain only two Chl molecules, so that they are spectroscopically equivalent to monomers of native-trimeric-PCP and do not aggregate further. Through removal of ensemble averaging we are able to observe for single reconstituted PCP complexes two clear steps in fluorescence intensity timetraces attributed to subsequent bleaching of the two Chl molecules. Importantly, the bleaching of the first Chl affects neither the energy nor the intensity of the emission of the second one. Since in strongly interacting systems Chl is a very efficient quencher of the fluorescence, this behavior implies that the two fluorescing Chls within a PCP monomer interact very weakly with each other which makes it possible to independently monitor the fluorescence of each individual chromophore in the complex. We apply this property, which distinguishes PCP from other light-harvesting systems, to measure the distribution of the energy splitting between two chemically identical Chl a molecules contained in the PCP monomer that reaches 280 cm− 1. In agreement with this interpretation, stepwise bleaching of fluorescence is also observed for native PCP complexes, which contain six Chls. Most PCP complexes reconstituted with both Chl a and Chl b show two emission lines, whose wavelengths correspond to the fluorescence of Chl a and Chl b. This is a clear proof that these two different chromophores are present in a single PCP monomer. Single molecule fluorescence studies of PCP complexes, both native and artificially reconstituted with chlorophyll mixtures, provide new and detailed information necessary to fully understand the energy transfer in this unique light-harvesting system.

Coherent anti-Stokes Raman scattering (CARS) microscopy is presented as a new nonlinear optical technique. The combination of vibrational spectroscopy and microscopy allows highly sensitive investigations of unlabelled samples. CARS is an ideal tool for studying a broad variety of samples. The main drawback of the technique is its non-zero-background nature, which implies that the signal has to be detected against a nonresonant background. The need to solve this problem is reflected in the rapid technological developments that have been observed during the last decade. Recent results show that CARS microscopy has the potential to become an important complementary technique that can be used with other well-established microscopic methods. Although it has some limitations, it offers unique access to many problems that cannot be tackled with conventional techniques. For this reason, it can be expected that the impressive growth of the field will continue.

Intercellular communication is a fundamental process in the development and functioning of multicellular organisms. Recently, an essentially new type of intercellular communication, based on thin membrane channels between cells, has been reported. These structures, termed intercellular or tunnelling nanotubes (TNTs), permit the direct exchange of various components or signals (e.g., ions, proteins, or organelles) between non-adjacent cells at distances over 100 μm. Our studies revealed the presence of tunnelling nanotubes in microvascular endothelial cells (HMEC-1). The TNTs were studied with live cell imaging, environmental scanning electron microscopy (ESEM) and coherent anti-Stokes Raman scattering spectroscopy (CARS). Tunneling nanotubes showed marked persistence: the TNTs could connect cells over long distances (up to 150 μm) for several hours. Several cellular organelles were present in TNTs, such as lysosomes and mitochondria. Moreover, we could identify lipid droplets as a novel type of cargo in the TNTs. Under angiogenic conditions (VEGF treatment) the number of lipid droplets increased significantly. Arachidonic acid application not only increased the number of lipid droplets but also tripled the extent of TNT formation. Taken together, our results provide the first demonstration of lipid droplets as a cargo of TNTs and thereby open a new field in intercellular communication research.

We report the results of coincidence counting experiments at the output of a Michelson interferometer using the zero-phonon-line emission of a single molecule at 1.4 K. Under continuous wave excitation, we observe the absence of coincidence counts as an indication of two-photon interference. This corresponds to the observation of Hong-Ou-Mandel correlations., Deutsche Forschungsgemeinschaft; Alexander von Humboldt Foundation (A.K.). O.E.M; Turkish Academy of Sciences (TÜBA)/GEBIP

Phycoerythrocyanin (PEC) is part of the phycobilisome of cyanobacteria. Its monomer carries one phycoviolobilin and two phycocyanobilins (PCB) as chromophores. For an understanding of the complicated energy transfer in phycobilisomes, a detailed knowledge of the processes in the constituting building proteins is indispensable. We report the experimental data necessary for the description of Förster energy transfer in monomeric PEC, including fluorescence lifetimes and quantum yields of the two subunits. The bulk experiments are complemented by studies of single PEC molecules. Förster energy calculations and Monte Carlo simulations based on the bulk data are presented. They reveal that earlier experimental findings of energy transfer heterogeneities in single PEC molecules originate in spectral shifts between the contributing chromophores.

Phycoerythrocyanin (PEC) is part of the light harvesting system of cyanobacteria. The PEC monomer contains one phycoviolobilin chromophore, which transfers excitation energy onto two phycocyanobilin chromophores. Many spectroscopical methods have been used in the past to study the bulk properties of PEC. These methods average over many molecules. Therefore, differences in the behavior of individual molecules remain hidden. The energy transfer within photosynthetic complexes is however sensitive to changes in the spectroscopic properties of the participating subunits. Knowledge about heterogeneities is therefore important for the description of the energy transfer in photosynthetic systems. Here, the recording of the fluorescence emission of single PEC molecules is used as a tool to obtain such information. Spectrally resolved detection as well as double resonance excitation of single PEC molecules is used to investigate their bleaching behavior. The trans isomer of the phycoviolobilin chromophore is identified as a short-lived dark state of monomeric PEC. Polarization sensitive single molecule detection is used for the direct observation of the energy transfer in individual PEC molecules. The experiments reveal that more than one-half of the PEC molecules exhibit an energy transfer behavior significantly different from the bulk. These heterogeneities persist on a time scale of several seconds. Model calculations lead to the conclusion that they are caused by minor shifts in the spectra of the chromophores.

Polymer chemistry 5(8), 2700-2703 (2014). doi:10.1039/c3py01684f, Published by RSC Publ., Cambridge

Water-soluble derivatives of pyrrolopyrrole cyanines (PPCys) have been synthesized by a post-synthetic modification route. In highly polar media, these dyes are excellent NIR fluorophores. Labeling experiments show how these novel dyes are internalized into mammalian cells.

Polymeric nano- and microparticles are finding widespread applications in materials and biological science. In all preparation methods pursued to date, the chemical stability of the particles is determined by the polymer system chosen. Usually, after particle synthesis, postprocessing with the aim of changing their stability is not possible. Therefore, one only has two choices: the synthesis of crosslinked polymer particles with high solvent and heat resistance and limited formability, or the synthesis of polymer particles consisting of linear polymer chains exhibiting low stability and high formability. In this contribution, we describe a new class of colloids which combine the advantages of both particle systems. The particles are composed of linear PMMA chains which are functionalized with photo-crosslinkable moieties. After preparation, the particles can be deformed before they are crosslinked by UV illumination. This offers unique possibilities for particle modification with a broad range of possible applications. Three examples are given. First, we show that the particles can be thermo-mechanically deformed into anisotropic shapes, in which they can be locked by subsequent crosslinking. Relaxation into the thermodynamically favorable spherical shape is thus suppressed, even in harsh environments. Second, we describe how the difference in solvent stability between illuminated and non-illuminated particles can be exploited for photolithography. Third, we demonstrate how photo-crosslinked anisotropic particles can be loaded with functional compounds, e.g. fluorophores.

Super-resolution three-dimensional (3D) optical microscopy has incomparable advantages over other high-resolution microscopic technologies, such as electron microscopy and atomic force microscopy, in the study of biological molecules, pathways and events in live cells and tissues. We present a novel approach of structured illumination microscopy (SIM) by using a digital micromirror device (DMD) for fringe projection and a low-coherence LED light for illumination. The lateral resolution of 90 nm and the optical sectioning depth of 120 μm were achieved. The maximum acquisition speed for 3D imaging in the optical sectioning mode was 1.6×10(7) pixels/second, which was mainly limited by the sensitivity and speed of the CCD camera. In contrast to other SIM techniques, the DMD-based LED-illumination SIM is cost-effective, ease of multi-wavelength switchable and speckle-noise-free. The 2D super-resolution and 3D optical sectioning modalities can be easily switched and applied to either fluorescent or non-fluorescent specimens.

Optical microscopy is an indispensable tool that is driving progress in cell biology. It still is the only practical means of obtaining spatial and temporal resolution within living cells and tissues. Most prominently, fluorescence microscopy based on dye-labeling or protein fusions with fluorescent tags is a highly sensitive and specific method of visualizing biomolecules within sub-cellular structures. It is however severely limited by labeling artifacts, photo-bleaching and cytotoxicity of the labels. Coherent Raman Scattering (CRS) has emerged in the last decade as a new multiphoton microscopy technique suited for imaging unlabeled living cells in real time with high three-dimensional spatial resolution and chemical specificity. This technique has proven to be particularly successful in imaging unstained lipids from artificial membrane model systems, to living cells and tissues to whole organisms. In this article, we will review the experimental implementations of CRS microscopy and their application to imaging lipids. We will cover the theoretical background of linear and non-linear vibrational micro-spectroscopy necessary for the understanding of CRS microscopy. The different experimental implementations of CRS will be compared in terms of sensitivity limits and excitation and detection methods. Finally, we will provide an overview of the applications of CRS microscopy to lipid biology.

We report the observation of ultralong coherence times in the purely electronic zero-phonon line emission of single terrylenediimide molecules at 1.4 K. Vibronic excitation and spectrally resolved detection with a scanning Fabry-Perot spectrum analyzer were used to measure a linewidth of 65 MHz. This is within a factor of 1.6 of the transform limit. It therefore indicates that single molecule emission may be suited for applications in linear optics quantum computation. Additionally it is shown that high resolution spectra taken with the spectrum analyzer allow for the investigation of fast spectral dynamics in the emission of a single molecule., Comment: to appear in Applied Physics Letters

We demonstrate a method for broadband laser pulse characterization based on a spectrally resolved cross-correlation with a narrowband flat-top gate pulse. Excellent phase-matching by collinear excitation in a microscope focus is exploited by degenerate four-wave mixing in a microscope slide. Direct group delay extraction of an octave spanning spectrum which is generated in a highly nonlinear fiber allows for spectral phase retrieval. The validity of the technique is supported by the comparison with an independent second-harmonic fringe-resolved autocorrelation measurement for an 11 fs laser pulse.

A series of novel pyrrolopyrrole cyanines (PPCys) bearing various aminophenyl substituents at the diketopyrrolopyrrole (DPP) core are presented. Compared to their alkoxyphenyl substituted analogues, these dyes feature additional intense electronic transitions of charge-transfer character which give detailed insight into the optical properties of PPCys. The energetic mixing of the involved orbitals has pronounced effects on the absorption and fluorescence behavior. Protonation of the amino function suppresses these effects and leads to a pronounced increase in fluorescence quantum yield. The photophysics of the dyes can be rationalized by means of a simple energy scheme.

Monitoring of the formation of stable fluorescent nanoparticles from controlled mixing of a THF solution of poly(fluorene ethynylene)-block-poly(ethylene glycol) in a microfluidic laminar flow crossjunction by spatially resolved fluorescence spectroscopy reveals the time scale of particle formation as well as incorporation of small molecule guests and the role of solvent mixing.