Kalina Peneva

Max Planck Institute for Polymer Research, Mayence, Rheinland-Pfalz, Germany

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Publications (26)105.88 Total impact

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    Small 12/2014; · 7.82 Impact Factor
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    ABSTRACT: 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. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
    Small (Weinheim an der Bergstrasse, Germany). 12/2014;
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    ABSTRACT: Release of siRNA from nanoscale polyplexes is a crucial yet little investigated process, important during all stages of therapeutic research. Here we develop new methods to characterize polyplex stability early on in the development of new materials. We used double fluorescent labeled siRNA to compare binding and stability of a panel of chemically highly diverse nanoscale polyplexes, including peptides, lipids, nanohydrogels, poly-L-lysine brushes, HPMA block copolymers and manganese oxide particles. Conventional EMSA and heparin competition methods were contrasted with a newly developed microscale thermophoresis (MST) assay, a near-equilibrium method that allows free choice of buffer conditions. Integrity of FRET-labeled siRNA was monitored in the presence of nucleases, in cell culture medium and inside living cells. This approach characterizes all relevant steps from polyplex stability, over uptake to in vitro knockdown capability. Diverging polyplex binding properties revealed drawbacks of conventional EMSA and heparin competition assays, where MST and FRET-based siRNA integrity measurements offered a better discrimination of differential binding strength. Since cell culture medium left siRNA in all polyplexes essentially intact, the relevant degradation events could be pinpointed to occur inside cells. Differential binding strength of the variegated polyplexes correlated only partially with intracellular degradation. The most successful compounds in RNAi showed intermediate binding strength in our assays. We introduce new methods for the efficient and informative characterization of siRNA polyplexes with special attention to stability. Comparing FRET-labeled siRNA in different polyplexes associates successful knockdown with intermediate siRNA stability in various steps from formulation to intracellular persistence.
    Pharmaceutical research. 12/2014;
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    ABSTRACT: In this study we describe the synthesis of novel functional non-nucleoside adenylyl cyclase inhibitors, which can be easily modified with thiol containing biomolecules such as tumour targeting structures. The linkage between inhibitor and biomolecule contains cleavable bonds to enable efficient intracellular delivery in the reductive milieu of the cytosol as well as in the acidic environment within endosomes and lysosomes. The suitability of this synthetic approach was shown by the successful bioconjugation of a poor cell permeable inhibitor with a cell penetrating peptide. Additionally, we have demonstrated the excellent inhibitory effect of the compounds presented here in a live-cell Förster resonance energy transfer-based assay in human embryonic kidney cells.This article is protected by copyright. All rights reserved.
    Chemical Biology &amp Drug Design 10/2014; · 2.47 Impact Factor
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    ABSTRACT: Here, the preparation of a novel block copolymer consisting of a statistical copolymer N-(2-hydroxypropyl) methacrylamide-s-N-(3-aminopropyl) methacrylamide and a short terminal 3-guanidinopropyl methacrylamide block is reported. This polymer structure forms neutral but water-soluble nanosized complexes with siRNA. The siRNA block copolymer complexes are first analyzed using agarose gel electrophoresis and their size is determined with fluorescence correlation spectroscopy. The protective properties of the polymer against RNA degradation are investigated by treating the siRNA block copolymer complexes with RNase V1. Heparin competition assays confirm the efficient release of the cargo in vitro. In addition, the utilization of microscale thermophoresis is demonstrated for the determination of the binding strength between a fluorescently labeled polyanion and a polymer molecule.
    Macromolecular Rapid Communications 04/2014; · 4.93 Impact Factor
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    ABSTRACT: 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 © 2014 European Peptide Society and John Wiley & Sons, Ltd.
    Journal of Peptide Science 02/2014; · 2.07 Impact Factor
  • Marco Lelle, Kalina Peneva
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    ABSTRACT: We describe the synthesis and characterization of a new lysine-based heterofunctional cross-linking reagent. It carries two readily available aminooxy functionalities and an activated and protected thiol group that is capable of generating reducible disulfides, the former enable bioorthogonal modification of ketones and aldehydes by the formation of an oxime bond. The efficacy of the linker was proven by coupling two doxorubicin molecules to the functionalized amino acid core and the subsequent bioconjugation of this drug conjugate with a thiolated antibody.
    Amino Acids 02/2014; · 3.91 Impact Factor
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    ABSTRACT: Polypeptides are successfully incorporated into poly(L-lactide) (PLLA) chains in a ring-opening polymerization (ROP) of L-lactide by using them as initiators. The resulting ABA triblock copolymers possess molecular weights up to 11000 g∙mol(-1) and polydispersities as low as 1.13, indicating the living character of the polymerization process. In a non-aqueous emulsion, peptide-initiated polymerization of L-lactide leads to well-defined nanoparticles, consisting of PLLA-block-peptide-block-PLLA copolymer. These nanoparticles are easily loaded by dye-encapsulation and transferred into aqueous media without aggregation (average diameter of 100 nm) or significant dye leakage. Finally, internalization of PLLA-block-peptide-block-PLLA nanoparticles by HeLa cells is demonstrated by a combination of coherent anti-Stokes Raman spectroscopy (CARS) and fluorescence microscopy. This demonstrates the promise of their utilization as cargo delivery vehicles.
    Biomacromolecules 03/2013; · 5.37 Impact Factor
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    ABSTRACT: The two-dimensional diffusion of isolated molecular tracers at the water-n-alkane interface was studied with fluorescence correlation spectroscopy. The interfacial diffusion coefficients of larger tracers with a hydrodynamic radius of 4.0 nm agreed well with the values calculated from the macroscopic viscosities of the two bulk phases. However, for small molecule tracers with hydrodynamic radii of only 1.0 and 0.6 nm, notable deviations were observed, indicating the existence of an interfacial region with reduced effective viscosity and increased mobility.
    Physical Review E 01/2013; 87(1-1):012403. · 2.31 Impact Factor
  • ChemInform 02/2011; 42(7).
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    ABSTRACT: Dieser Aufsatz fasst die jüngsten Fortschritte auf dem Gebiet der Rylenfarbstoffe und Rylen-Nanoemitter für den Einsatz in der Photonik zusammen und beschreibt den Einfluss des Farbstoffdesigns auf die Leistungsmerkmale; im Zentrum stehen dabei die optischen Eigenschaften, die Selbstorganisation, die molekularen Wechselwirkungen sowie die Wechselwirkungsspezifität dieser Verbindungen. Die Messung ihrer Absorptions-, Emissions- oder Anregungsspektren ermöglicht die genaue Bestimmung der Position oder der dreidimensionalen Orientierung ihrer Übergangsdipolmomente. Wichtig ist hierbei das Wechselspiel zwischen maßgeschneidertem (makro)molekularem Design und Einzelmolekül-spektroskopischen Untersuchungen. Die experimentelle Verfolgung von Einzelmolekülen ermöglicht die Aufklärung komplexer Prozesse, z. B. der Kinetik von Energietransferprozessen oder der (Bio-)Katalyse, wodurch ein tieferes Verständnis der Entstehung und Herkunft von Unregelmäßigkeiten möglich wird. Derartige Untersuchungen sind für die Entwicklung verbesserter Nanoemitter unerlässlich und erfordern eine enge Zusammenarbeit von Spektroskopikern und Synthetikern.
    Angewandte Chemie 11/2010; 122(48).
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    ABSTRACT: Employing the utility of the native chemical ligation, site-specific attachment of an ultrastable perylene dye to a derivative of the major light-harvesting complex (LHCII) was demonstrated. Biochemical analysis of the conjugate indicated that the structure and function of LHCII remain largely unaffected by the N-terminal modification.
    Organic & Biomolecular Chemistry 11/2010; 8(21):4823-6. · 3.57 Impact Factor
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    ABSTRACT: 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.
    Angewandte Chemie International Edition 10/2010; 49(48):9068-93. · 11.34 Impact Factor
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    ABSTRACT: 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.
    Biophysical Journal 05/2010; 98(9):1873-82. · 3.67 Impact Factor
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    ABSTRACT: 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.
    The Journal of Physical Chemistry B 03/2009; 113(11):3355-9. · 3.61 Impact Factor
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    ABSTRACT: Exciton migration! Spectroscopic analyses and extensive molecular dynamics studies revealed a well-defined 4(1) helix in which the perylene molecules (see figure) form four "helter-skelter-like" overlapping pathways along which excitons and electrons can rapidly migrate.We report on a combined experimental and computational investigation on the synthesis and thorough characterization of the structure of perylene-functionalized polyisocyanides. Spectroscopic analyses and extensive molecular dynamics studies revealed a well defined 4(1) helix in which the perylene molecules form four "helter skelter-like" overlapping pathways along which excitons and electrons can rapidly migrate. The well-defined polymer scaffold stabilized by hydrogen bonding, to which the chromophores are attached, accounts for the precise architectural definition, and molecular stiffness observed for these molecules. Molecular-dynamics studies showed that the chirality present in these polymers is expressed in the formation of stable right-handed helices. The formation of chiral supramolecular structures is further supported by the measured and calculated bisignated Cotton effect. The structural definition of the chromophores aligned in one direction along the backbone is highlighted by the extremely efficient exciton migration rates and charge densities measured with Transient Absorption Spectroscopy.
    Chemistry - A European Journal 02/2009; 15(11):2536-47. · 5.93 Impact Factor
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    ABSTRACT: 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.
    Chemistry - A European Journal 02/2009; 15(7):1661-72. · 5.93 Impact Factor
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    ABSTRACT: 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.
    ChemPhysChem 01/2009; 10(1):151-61. · 3.35 Impact Factor
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    ABSTRACT: The electronic transport properties of stacks of perylene-bis(dicarboximide) (PDI) chromophores, covalently fixed to the side arms of rigid, helical polyisocyanopeptides, are studied using thin-film transistors. In device architectures where the transistor channel lengths are somewhat greater than the average polymer chain length, carrier mobilities of order 10 � 3 cm 2 V � 1 s � 1 at 350 K are found, which are limited by inter-chain transport processes. The influence of p-p interactions on the material properties is studied by using PDIs with and without bulky substituents in the bay area. In order to attain a deeper understanding of both the electronic and the electronic-transport properties of these systems, studies of self-assembly on surfaces are combined with electronic characterization using Kelvin probe force microscopy, and also a theoretical study of electronic coupling. The use of a rigid polymer backbone as a scaffold to achieve a full control over the position and orientation of functional groups is of general applicability and interest in the design of building blocks for technologically important functional materials, as well as in more fundamental studies of chromophoric interactions.
    Advanced Functional Materials 11/2008; 18(24):3947 - 3955. · 10.44 Impact Factor
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    ABSTRACT: 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.
    Journal of the American Chemical Society 05/2008; 130(16):5398-9. · 10.68 Impact Factor