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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., (© 2020 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.)

Suspensions of hard ellipsoidal particles exhibit complex phase behavior as shown by theoretical predictions and simulations of phase diagrams. Here, we report quantitative confocal microscopy experiments of hard prolate colloidal ellipsoids with different aspect ratio a/b. We studied different volume fractions φ of ellipsoids in density and refractive index matched suspensions. Large 3D sample volumes were investigated and the positions as well as the orientations of all ellipsoids were extracted by image analysis routines. By evaluating the translational and orientational order in the system we determined the presence of isotropic and nematic phases. For ellipsoids with a/b = 2.0 we found that isotropic phases form at all φ, while ellipsoids with a/b = 7.0 formed nematic phases at high φ, as expected from theory and simulations. For a/b = 3.5 and a/b = 4.1, however, we observed the absence of long-range orientational order even at φ where nematic phases are expected. We show that local orientational order formed with the emergence of nematic precursors for a/b = 3.5 and short-ranged nematic domains for a/b = 4.1. Our results provide novel insight into the phase behavior and orientational order of ellipsoids with different aspect ratios.

Abundant post-translational modification through methylation alters the function, stability, and/or localization of a protein. Malfunctions in post-translational modification are associated with severe diseases. To unravel protein methylation sites and their biological functions, chemical methylation reporters have been developed. However, until now, their usage was limited to cell lysates. Herein, we present the first generally applicable approach for imaging methylation of individual proteins in human cells, which is based on a combination of chemical reporter strategies, bioorthogonal ligation reactions, and FRET detected by means of fluorescence lifetime imaging microscopy. Through this approach, methylation of histone 4 and the non-histone proteins tumor suppressor p53, kinase Akt1, and transcription factor Foxo1 in two human cell lines has been successfully imaged. To further demonstrate its potential, the localization-dependent methylation state of Foxo1 in the cellular context has been visualized., (© 2019 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.)

We present a simple Yb fiber pumped source for narrow bandwidth picosecond pulses which are tunable in the visible spectral region. This emission is obtained by frequency doubling of a soliton generated in a photonic crystal fiber. The system is attractive for different types of nonlinear optical microscopy and can easily be adapted to meet different experimental prerequisites. As an example, we demonstrate coherent anti-Stokes Raman scattering microscopy using the laser source described.

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., (© 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.)

Posttranslational protein glycosylation is conserved in all kingdoms of life and implicated in the regulation of protein structure, function, and localization. The visualization of glycosylation states of designated proteins within living cells is of great importance for unraveling the biological roles of intracellular protein glycosylation. Our generally applicable approach is based on the incorporation of a glucosamine analog, Ac 4 GlcNCyoc, into the cellular glycome via metabolic engineering. Ac 4 GlcNCyoc can be labeled in a second step via inverse-electron-demand Diels-Alder chemistry with fluorophores inside living cells. Additionally, target proteins can be expressed as enhanced green fluorescent protein (EGFP)-fusion proteins. To assess the proximity of the donor EGFP and the glycan-anchored acceptor fluorophore, Förster resonance energy transfer (FRET) is employed and read out with high contrast by fluorescence lifetime imaging (FLIM) microscopy. In this chapter, we present a detailed description of methods required to perform protein-specific imaging of glycosylation inside living cells. These include the complete synthesis of Ac 4 GlcNCyoc, immunoprecipitation of EGFP-fusion proteins to examine the Ac 4 GlcNCyoc modification state, and a complete section on basics, performance, as well as data analysis for FLIM-FRET microscopy. We also provide useful notes necessary for reproducibility and point out strengths and limitations of the approach., (© 2018 Elsevier Inc. All rights reserved.)

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., (© 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)

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., (© 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)

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 ~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.

Protein glycosylation is a ubiquitous post-translational modification that is involved in the regulation of many aspects of protein function. In order to uncover the biological roles of this modification, imaging the glycosylation state of specific proteins within living cells would be of fundamental importance. To date, however, this has not been achieved. Herein, we demonstrate protein-specific detection of the glycosylation of the intracellular proteins OGT, Foxo1, p53, and Akt1 in living cells. Our generally applicable approach relies on Diels-Alder chemistry to fluorescently label intracellular carbohydrates through metabolic engineering. The target proteins are tagged with enhanced green fluorescent protein (EGFP). Förster resonance energy transfer (FRET) between the EGFP and the glycan-anchored fluorophore is detected with high contrast even in presence of a large excess of acceptor fluorophores by fluorescence lifetime imaging microscopy (FLIM)., (© 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)

Raman spectroscopy offers great promise for label free imaging in biomedical applications. Its use, however, is hampered by the long integration times required and the presence of autofluorescence in many samples which outshines the Raman signals. In order to overcome these limitations, a variety of different non-linear Raman imaging techniques have been developed over the last decade. This review describes biomedical applications of these novel but already mature imaging techniques., (Copyright © 2015 Elsevier B.V. All rights reserved.)

The reaction of POCl3-activated, readily soluble diketopyrrolopyrrole (DPP) with 2-aminoheteroaromatics to yield 1:1 and 1:2 hydrogen chelates is described. Complexation of these hydrogen chelates with boron reagents results in thermally and photochemically stable fluorescent dyes (PP-azacyanines). The 1:2 complexes in particular absorb at long wavelengths and are brightly fluorescing. The rich photophysics of the new compounds are presented. Both the pronounced vibrational fine structure of the S0 → S1 transitions and the observed fluorescence phenomena allow detailed conclusions to be made on the correlation between molecular structure and optical properties., (© 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)

We present experimental results regarding the effects of electric pulses on giant unilamellar vesicles (GUVs). We have used phase contrast and coherent anti-Stokes Raman scattering (CARS) microscopy as relevant optical approaches to gain insight into membrane changes under electropermeabilization. No addition of exogenous molecules (lipid analogue, fluorescent dye) was needed. Therefore, experiments were performed on pure lipid systems avoiding possible artefacts linked to their use. Structural membrane changes were assessed by loss of contrast inside the GUVs due to sucrose and glucose mixing. Our observations, performed at the single vesicle level, indicate these changes are under the control of the number of pulses and field intensity. Larger number of pulses enhances membrane alterations. A threshold value of the field intensity must be applied to allow exchange of molecules between GUVs and the external medium. This threshold depends on the size of the vesicles, the larger GUVs being affected at lower electric field strengths than the smaller ones. Our experimental data are well described by a simple model in which molecule entry is driven by direct exchange. The CARS microscopic study of the effect of pulse duration confirms that pulses, in the ms time range, induce loss of lipids and membrane deformations facing the electrodes., (Copyright © 2012 Elsevier B.V. All rights reserved.)

The delivery of therapeutic molecules such as plasmid DNA in cells and tissues by means of electric fields holds great promise for anticancer treatment. To allow for their therapeutic action, the molecules have first to traverse the cell membrane. The mechanisms by which the electrotransferred pDNA interacts with and crosses the plasma membrane are not yet fully explained. The aim of this study is to unravel the role of cholesterol during gene electrotransfer in cells. We performed cholesterol depletion experiments and measured its effects on various steps of the electroporation process. The first two steps consisting of electropermeabilization of the plasma membrane and of pDNA interaction with it were not affected by cholesterol depletion. In contrast, gene expression decreased. Colocalization studies with endocytotic markers showed that pDNA is endocytosed with concomitant clathrin- and caveolin/raft-mediated endocytosis. Cholesterol might be involved in the pDNA translocation through the plasma membrane. This is the first direct experimental evidence of the occurrence of endocytosis in gene electrotransfer., (Copyright © 2011 Elsevier B.V. All rights reserved.)

Pyrrolopyrrole cyanine (PPCy) dyes are presented as a novel class of near-infrared (NIR) chromophores, which are synthesized in a condensation reaction of diketopyrrolopyrrole with heteroarylacetonitrile compounds. Their optical properties are marked by strong and narrow-band NIR absorptions. Complexation products with BF(2) and BPh(2) show strong NIR fluorescence and hardly any absorption in the visible range. We synthesized a series of new PPCys that differ only in the heterocyclic peripheral groups of the chromophore. With this strategy, the absorption spectra can be tuned between 684 and 864 nm, while high fluorescence quantum yields are maintained. The influence of the heterocycle on the optical properties of the dyes is discussed.

A series of unusual dinuclear mu2-(eta2-NO)-nitrosoaniline-bridged complexes [[(CO)3Re(mu-X)]2ONC6H4NR2] (X = Cl, Br, I; R = Me, Et) with dichroic properties have been synthesised by reaction of pentacarbonylhalogenorhenium(I) [(CO)5ReX] (X = Cl, Br, I) with the corresponding nitrosoaniline derivatives R2NC6H4NO (R = Me, Et). The deeply coloured solutions in CH2Cl2 show broad UV/Vis absorptions from 595 to 620 nm depending on the halogen bridges and N substituents. Single crystals of all six compounds exhibit a pronounced linear dichroism. The molecular structures have been determined by single-crystal X-ray analyses. All the compounds contain two face-shared octahedra, with two halogens and one NO ligand as bridges. The NO ligand coordinates in a nonsymmetrical eta2-like fashion with N or O coordination to each Re centre. Therefore, the C-nitroso group and the planar NC2 moiety of NR2 both lie almost exactly within the symmetry plane of the dinuclear complexes. These complexes belong to the novel and simple class of neutral dinuclear C-nitroso complexes that include the rare, non-assisted mu2-(eta2-NO) ligand function and have only single halogen atoms in bridging positions.

Much effort has been dedicated to the design of significantly red shifted variants of the green fluorescent protein (GFP) from Aequoria victora (av). These approaches have been based on classical engineering with the 20 canonical amino acids. We report here an expansion of these efforts by incorporation of an amino substituted variant of tryptophan into the "cyan" GFP mutant, which turned it into a "gold" variant. This variant possesses a red shift in emission unprecedented for any avFP, similar to "red" FPs, but with enhanced stability and a very low aggregation tendency. An increasing number of non-natural amino acids are available for chromophore redesign (by engineering of the genetic code) and enable new general strategies to generate novel classes of tailor-made GFP proteins.