Kalina Peneva

The Rylene Colorant Family—Tailored Nanoemitters for Photonics Research and Applications

This Review summarizes the latest advances in the field of rylene dyes and rylene nanoemitters for applications in photonics, and describes the influence of the dye design on the optical properties, the self-assembly, the molecular interactions, as well as the labeling specificity of the compounds. The interplay between tailored (macro)molecular design and bulk/single-molecule spectroscopy enables complex processes to be explained, for example, the kinetics of energy-transfer processes or (bio)catalysis. Such investigations are essential for the ultimate design of optimized nanoemitters, and require a close cooperation between spectroscopists and preparative organic chemists.

Exploiting the Nitrilotriacetic Acid Moiety for Biolabeling with Ultrastable Perylene Dyes

Fluorescent probes are essential for the exploration of protein function, detection of molecular interactions, and conformational changes. The nitrilotriacetic acid derivatives of different chromophores were successfully used for site-selective noncovalent fluorescence labeling of histidine-tagged proteins. All of them, however, suffer from the same drawback--loss of the fluorescence upon binding of the nickel ions. Herein we present the solution and solid phase synthesis of water-soluble perylene(dicarboximide) functionalized with a nitrilotriacetic acid moiety (PDI-NTA). The photophysical properties of PDI-NTA revealed an exceptional photostability and fluorescence quantum yield that remained unchanged upon addition of nickel ions. The F1 complex of F0F1-ATP synthase from Escherichia coli, containing three hexahistidine tags, was labeled and the suitability for site-specific labeling of the new chromophore demonstrated using fluorescence correlation spectroscopy.

Diffusion in Polymer Solutions Studied by Fluorescence Correlation Spectroscopy

We employed fluorescence correlation spectroscopy (FCS) to study the diffusion of molecular and macromolecular tracers in polystyrene solutions over a broad range of concentrations (c) and molecular weights (M(w,m)) of the matrix polymer. Molecular tracer diffusion scales only with the matrix concentration and superimposes on a single, nonpolymer specific, curve. On the contrary, the diffusion of macromolecular tracers in solutions of matrix polymers with M(w,m) sufficiently larger than the tracer molecular weight scales with c/c(p)*, where c(p)* is the tracer overlap concentration. We further demonstrate that FCS can address local and global dynamics simultaneously.

Linking Phospholipase Mobility to Activity by Single-Molecule Wide-Field Microscopy

Many of the biological processes taking place in cells are mediated by enzymatic reactions occurring in the cell membrane. Understanding interfacial enzymatic catalysis is therefore crucial to the understanding of cellular function. Unfortunately, a full picture of the overall mechanism of interfacial enzymatic catalysis, and particularly the important diffusion processes therein, remains unresolved. Herein we demonstrate that single-molecule wide-field fluorescence microscopy can yield important new information on these processes. We image phospholipase enzymes acting upon bilayers of their natural phospholipid substrate, tracking the diffusion of thousands of individual enzymes while simultaneously visualising local structural changes to the substrate layer. We study several enzyme types with different affinities and catalytic activities towards the substrate. Analysis of the trajectories of each enzyme type allows us successfully to correlate the mobility of phospholipase with its catalytic activity at the substrate. The methods introduced herein represent a promising new approach to the study of interfacial/heterogeneous catalysis systems.

Photophysics of New Water-Soluble Terrylenediimide Derivatives and Applications in Biology

The photophysical properties of three new water-soluble terrylenediimide (WS-TDI) derivatives are investigated and their utilization in biological experiments is demonstrated. Each of these dyes can be excited in the far red region of the visible spectrum, making them good candidates for in-vivo studies. Single-molecule techniques characterize their photophysics that is, the number of emitted photons, blinking characteristics and survival times until photobleaching takes place. All three dyes exhibit bright fluorescence, as well as an extremely high resistance against photodegradation compared to other well-known fluorophores. Due to their different characteristics the three new WS-TDI derivatives are suitable for specialized biological applications. WS-TDI dodecyl forms non-fluorescent aggregates in water which can be disrupted in a hydrophobic environment leading to a monomeric fluorescent form. Due to its high lipophilicity WS-TDI dodecyl anchors efficiently in lipid bilayers with its alkyl chain and hence can be ideally used to image membranes and membrane-containing compartments in living cells. In contrast, the positively charged WS-TDI pyridoxy is a new type of chromophore in the WS-TDI family. It is fully solubilized in water forming fluorescent monomers and is successfully used to label the envelope of herpes simplex viruses. Finally, it is shown that a WS-TDI derivative functionalized with N-hydroxysuccinimide ester moiety (WS-TDI/NHS ester) provides a versatile reactive dye molecule for the specific labelling of amino groups in biomolecules such as DNA.

Influence of Lipid Heterogeneity and Phase Behavior on Phospholipase A2 Action at the Single Molecule Level

We monitored the action of phospholipase A(2) (PLA(2)) on L- and D-dipalmitoyl-phosphatidylcholine (DPPC) Langmuir monolayers by mounting a Langmuir-trough on a wide-field fluorescence microscope with single molecule sensitivity. This made it possible to directly visualize the activity and diffusion behavior of single PLA(2) molecules in a heterogeneous lipid environment during active hydrolysis. The experiments showed that enzyme molecules adsorbed and interacted almost exclusively with the fluid region of the DPPC monolayers. Domains of gel state L-DPPC were degraded exclusively from the gel-fluid interface where the buildup of negatively charged hydrolysis products, fatty acid salts, led to changes in the mobility of PLA(2). The mobility of individual enzymes on the monolayers was characterized by single particle tracking. Diffusion coefficients of enzymes adsorbed to the fluid interface were between 3.2 microm(2)/s on the L-DPPC and 4.9 microm(2)/s on the D-DPPC monolayers. In regions enriched with hydrolysis products, the diffusion dropped to approximately 0.2 microm(2)/s. In addition, slower normal and anomalous diffusion modes were seen at the L-DPPC gel domain boundaries where hydrolysis took place. The average residence times of the enzyme in the fluid regions of the monolayer and on the product domain were between approximately 30 and 220 ms. At the gel domains it was below the experimental time resolution, i.e., enzymes were simply reflected from the gel domains back into solution.

Water-Soluble NIR-Absorbing Rylene Chromophores for Selective Staining of Cellular Organelles.

Biocompatible organic dyes emitting in the near-infrared are highly desirable in fluorescence imaging techniques. Herein we report a synthetic approach for building novel small peri-guanidine-fused naphthalene monoimide and perylene monoimide chromophores. The presented structures possess near-infrared absorption and emission, high photostability, and good water solubility. After a fast cellular uptake, they selectively stain mitochondria with a low background in live and fixed cells. They can be additionally modified in a one-step reaction with functional groups for covalent labeling of proteins. The low cytotoxicity allows a long time exposure of live cells to the dyes without the necessity of washing. Successful application in localization super-resolution microscopy was demonstrated in phosphate-buffered saline without any reducing or oxidizing additives.

Particle-Based Optical Sensing of Intracellular Ions at the Example of Calcium - What Are the Experimental Pitfalls?

Colloidal particles with fluorescence read-out are commonly used as sensors for the quantitative determination of ions. Calcium, for example, is a biologically highly relevant ion in signaling, and thus knowledge of its spatio-temporal distribution inside cells would offer important experimental data. However, the use of particle-based intracellular sensors for ion detection is not straightforward. Important associated problems involve delivery and intracellular location of particle-based fluorophores, crosstalk of the fluorescence read-out with pH, and spectral overlap of the emission spectra of different fluorophores. These potential problems are outlined and discussed here with selected experimental examples. Potential solutions are discussed and form a guideline for particle-based intracellular imaging of ions.

Tuning Single‐Molecule Dynamics in Functionalized Mesoporous Silica

Mesoporous silica materials are promising host structures for diverse applications in nanoscience. Many applications can profit significantly from the ability to influence guest dynamics in the host matrix. To this end, we introduce covalently attached organic functionalization into the walls of mesoporous silica networks. Using single-molecule fluorescence microscopy, we study the diffusion behavior of single terrylene diimide dye molecules in functionalized mesoporous silica films. We show that, through variation of the chemical nature and density of the functional groups, the diffusion dynamics of the dye molecules, in the presence of the surfactant template, can be controlled precisely. The mean diffusion coefficient of the dye molecules increases or decreases depending on the functional group attached to the silica wall. This allows fine-tuning of the diffusion dynamics of the dye by approximately one order of magnitude. The observed changes in the mean diffusion coefficients can be explained by shielding of hydroxyl groups on the silica surface in combination with changes in the rigidity of the micellar packing in the film, as well as direct interactions between the functional groups and the dye molecules.

Novel cleavable cell-penetrating peptide–drug conjugates: synthesis and characterization

We report the first drug conjugate with a negatively charged amphipathic cell‐penetrating peptide. Furthermore, we compare two different doxorubicin cell‐penetrating peptide conjugates, which are both unique in their properties, due to their net charge at physiological pH, namely the positively charged octaarginine and the negatively charged proline‐rich amphipathic peptide. These conjugates were prepared exploiting a novel heterobifunctional crosslinker to join the N‐terminal cysteine residue of the peptides with the aliphatic ketone of doxorubicin. This small linker contains an activated thiol as well as aminooxy functionality, capable of generating a stable oxime bond with the C‐13 carbonyl group of doxorubicin. The disulfide bond formed between the peptide and doxorubicin enables the release of the drug in the cytosol, as confirmed by drug‐release studies performed in the presence of glutathione. Additionally, the cytotoxicity as well as the cellular uptake and distribution of this tripartite drug delivery system was investigated in MCF‐7 and HT‐29 cell lines. Copyright