TY - JOUR A1 - Eisold, Ursula A1 - Sellrie, Frank A1 - Memczak, Henry A1 - Andersson, Anika A1 - Schenk, Jörg A. A1 - Kumke, Michael Uwe T1 - Dye tool box for a fluorescence enhancement immunoassay JF - Bioconjugate chemistry N2 - Immunochemical analytical methods are very successful in clinical diagnostics and are nowadays also emerging in the control of food as well as monitoring of environmental issues. Among the different immunoassays, luminescence based formats are characterized by their outstanding sensitivity making this format especially attractive for future applications. The need for multiparameter detection capabilities calls for a tool box of dye labels in order to transduce the biochemical reaction into an optically detectable signal. Here, in a multiparameter approach each analyte may be detected by a different dye with a unique emission color (covering the blue to red spectral range) or a unique luminescence decay kinetics. In the case of a competitive immunoassay format for each of the different dye labels an individual antibody would be needed. In the present paper a slightly modified approach is presented using a 7-aminocoumarin unit as the basic antigen against which highly specific antibodies were generated. Leaving the epitope region in the dyes unchanged but introducing a side group in positon 3 of the coumarin system allowed us to tune the optical properties of the coumarin dyes without the necessity of new antibody generation. Upon modification of the parent coumarin unit the full spectral range from blue to deep red was accessed. In the manuscript the photophysical characterization of the coumarin derivatives and their corresponding immunocomplexes with two highly specific antibodies is presented. The coumarin dyes and their immunocomplexes were characterized by steady-state and time-resolved absorption as well as emission spectroscopy. Moreover, fluorescence depolarization measurements were carried out to complement the data stressing the different binding modes of the two antibodies. The binding modes were evaluated using the photophysics of 7-aminocoumarins and how it was affected in the respective immunocomplexes, namely, the formation of the intramolecular charge transfer (ICT) as well as the twisted intramolecular charge transfer (TICT). In contrast to other antibody-dye pairs reported a distinct fluorescence enhancement upon formation of the antibody-dye complex up to a factor of SO was found. Because of the easy emission color tuning by tailoring the coumarin substitution for the antigen binding in nonrelevant position 3 of the parent molecule, a dye tool box is on hand which can be used in the construction of competitive multiparameter fluorescence enhancement immunoassays (FenIA). Y1 - 2018 U6 - https://doi.org/10.1021/acs.bioconjchem.7b00731 SN - 1043-1802 VL - 29 IS - 1 SP - 203 EP - 214 PB - American Chemical Society CY - Washington ER - TY - JOUR A1 - Kupstat, Annette A1 - Ritschel, Thomas A1 - Kumke, Michael Uwe T1 - Oxazine Dye-Conjugated DNA Oligonucleotides Forster Resonance Energy Transfer in View of Molecular Dye-DNA Interactions JF - Bioconjugate chemistry N2 - In this work, the photophysical properties of two oxazine dyes (ATTO 610 and ATTO 680) covalently attached via a C6-amino linker to the 5'-end of short single-stranded as well as double-stranded DNA (ssDNA and dsDNA, respectively) of different lengths were investigated. The two oxazine dyes were chosen because of the excellent spectral overlap, the high extinction coefficients, and the high fluorescence quantum yield of ATTO 610, making them an attractive Forster resonance energy transfer (FRET) pair for bioanalytical applications in the far-red spectral range. To identify possible molecular dye-DNA interactions that cause photophysical alterations, we performed a detailed spectroscopic study, including time-resolved fluorescence anisotropy and fluorescence correlation spectroscopy measurements. As an effect of the DNA conjugation, the absorption and fluorescence maxima of both dyes were bathochromically shifted and the fluorescence decay times were increased. Moreover, the absorption of conjugated ATTO 610 was spectrally broadened, and a dual fluorescence emission was observed. Steric interactions with ssDNA as well as dsDNA were found for both dyes. The dye-DNA interactions were strengthened from ssDNA to dsDNA conjugates, pointing toward interactions with specific dsDNA domains (such as the top of the double helix). Although these interactions partially blocked the dye-linker rotation, a free (unhindered) rotational mobility of at least one dye facilitated the appropriate alignment of the transition dipole moments in doubly labeled ATTO 610/ATTO 680-dsDNA conjugates for the performance of successful FRET. Considering the high linker flexibility for the determination of the donor-acceptor distances, good accordance between theoretical and experimental FRET parameters was obtained. The considerably large Forster distance of similar to 7 nm recommends the application of this FRET pair not only for the detection of binding reactions between nucleic acids in living cells but also for monitoring interactions of larger biomolecules such as proteins. Y1 - 2011 U6 - https://doi.org/10.1021/bc200379y SN - 1043-1802 VL - 22 IS - 12 SP - 2546 EP - 2557 PB - American Chemical Society CY - Washington ER - TY - JOUR A1 - López de Guereñu, Anna A1 - Bastian, Philipp A1 - Wessig, Pablo A1 - John, Leonard A1 - Kumke, Michael Uwe T1 - Energy Transfer between Tm-Doped Upconverting Nanoparticles and a Small Organic Dye with Large Stokes Shift JF - Biosensors : open access journal N2 - Lanthanide-doped upconverting nanoparticles (UCNP) are being extensively studied for bioapplications due to their unique photoluminescence properties and low toxicity. Interest in RET applications involving UCNP is also increasing, but due to factors such as large sizes, ion emission distributions within the particles, and complicated energy transfer processes within the UCNP, there are still many questions to be answered. In this study, four types of core and core-shell NaYF4-based UCNP co-doped with Yb3+ and Tm3+ as sensitizer and activator, respectively, were investigated as donors for the Methyl 5-(8-decanoylbenzo[1,2-d:4,5-d ']bis([1,3]dioxole)-4-yl)-5-oxopentanoate (DBD-6) dye. The possibility of resonance energy transfer (RET) between UCNP and the DBD-6 attached to their surface was demonstrated based on the comparison of luminescence intensities, band ratios, and decay kinetics. The architecture of UCNP influenced both the luminescence properties and the energy transfer to the dye: UCNP with an inert shell were the brightest, but their RET efficiency was the lowest (17%). Nanoparticles with Tm3+ only in the shell have revealed the highest RET efficiencies (up to 51%) despite the compromised luminescence due to surface quenching. KW - resonance energy transfer KW - DBD dye KW - core shell UCNP KW - time-resolved luminescence Y1 - 2019 U6 - https://doi.org/10.3390/bios9010009 SN - 2079-6374 VL - 9 IS - 1 PB - MDPI CY - Basel ER - TY - JOUR A1 - Roethlein, Christoph A1 - Miettinen, Markus S. A1 - Borwankar, Tejas A1 - Buerger, Joerg A1 - Mielke, Thorsten A1 - Kumke, Michael Uwe A1 - Ignatova, Zoya T1 - Architecture of polyglutamine-containing fibrils from time-resolved fluorescence decay JF - The journal of biological chemistry N2 - The disease risk and age of onset of Huntington disease (HD) and nine other repeat disorders strongly depend on the expansion of CAG repeats encoding consecutive polyglutamines (polyQ) in the corresponding disease protein. PolyQ length-dependent misfolding and aggregation are the hallmarks of CAG pathologies. Despite intense effort, the overall structure of these aggregates remains poorly understood. Here, we used sensitive time-dependent fluorescent decay measurements to assess the architecture of mature fibrils of huntingtin (Htt) exon 1 implicated in HD pathology. Varying the position of the fluorescent labels in the Htt monomer with expanded 51Q (Htt51Q) and using structural models of putative fibril structures, we generated distance distributions between donors and acceptors covering all possible distances between the monomers or monomer dimensions within the polyQ amyloid fibril. Using Monte Carlo simulations, we systematically scanned all possible monomer conformations that fit the experimentally measured decay times. Monomers with four-stranded 51Q stretches organized into five-layered beta-sheets with alternating N termini of the monomers perpendicular to the fibril axis gave the best fit to our data. Alternatively, the core structure of the polyQ fibrils might also be a zipper layer with antiparallel four-stranded stretches as this structure showed the next best fit. All other remaining arrangements are clearly excluded by the data. Furthermore, the assessed dimensions of the polyQ stretch of each monomer provide structural evidence for the observed polyQ length threshold in HD pathology. Our approach can be used to validate the effect of pharmacological substances that inhibit or alter amyloid growth and structure. Y1 - 2014 U6 - https://doi.org/10.1074/jbc.M114.581991 SN - 0021-9258 SN - 1083-351X VL - 289 IS - 39 SP - 26817 EP - 26828 PB - American Society for Biochemistry and Molecular Biology CY - Bethesda ER - TY - JOUR A1 - Schäfer, Thorsten A1 - Huber, Florian A1 - Seher, Holger A1 - Missana, Tiziana A1 - Alonso, Ursula A1 - Kumke, Michael Uwe A1 - Eidner, Sascha A1 - Claret, Francis A1 - Enzmann, Frieder T1 - Nanoparticles and their influence on radionuclide mobility in deep geological formations JF - Applied geochemistry : journal of the International Association of Geochemistry and Cosmochemistry N2 - This article gives an overview of the current status of knowledge concerning the role of nanoparticles (inorganic and organic) in deep geological host rocks and the potential influence of these nanoparticles on radionuclide migration in far-field systems. The manuscript is not intended to be a full review paper or overview paper concerning nanoparticles, here the intention is to refer to recent publications but to highlight the progress made in the 6th framework project IP FUNMIG (Fundamental processes of radionuclide migration) and the open literature over the past 5 a concerning the process understanding of nanoparticle related issues in the three host rock formations investigated, namely: claystones, crystalline rocks and salt rock overburden. The results show inter alia that the inorganic nanoparticle concentration in deep groundwaters of advection dominated systems rarely exceeds 1 mg L (1) and is expected to be in the ng L (1) range in diffusion controlled systems. For organic nanoparticles DOC concentrations up to tens of milligrams in diffusion-controlled indurated clays with molecular sizes mostly <500 Da have been found. Fulvic acid type organics have been identified in crystalline environments and plastic Clay formations (Boom Clay) with molecular sizes <= 300 kDa. Additional sources of inorganic nanoparticles from the repository near-field (compacted bentonite) were identified and the initial erosion rates were determined. The results indicate under stagnant conditions similar to 38 mg cm (2) a (1) for bi-distilled water, similar to 20 mg cm (2) a (1) for glacial melt water (Grimsel groundwater) and very low rates similar to 0.02 mg cm (2) a (1) for 5 mM CaCl2 contact water. The low critical coagulation concentration (CCC) indicative for purely diffusion controlled coagulation of 1 mM L (1) Ca2+ found in bentonite nanoparticle stability analysis matches the low nanoparticle mobilization from compacted bentonite found in these systems. Y1 - 2012 U6 - https://doi.org/10.1016/j.apgeochem.2011.09.009 SN - 0883-2927 VL - 27 IS - 2 SP - 390 EP - 403 PB - Elsevier CY - Oxford ER -