@article{ChoiKotthoffOlejkoetal.2018, author = {Choi, Youngeun and Kotthoff, Lisa and Olejko, Lydia and Resch-Genger, Ute and Bald, Ilko}, title = {DNA origami-based forster resonance energy-transfer Nanoarrays and their application as ratiometric sensors}, series = {ACS applied materials \& interfaces}, volume = {10}, journal = {ACS applied materials \& interfaces}, number = {27}, publisher = {American Chemical Society}, address = {Washington}, issn = {1944-8244}, doi = {10.1021/acsami.8b03585}, pages = {23295 -- 23302}, year = {2018}, abstract = {DNA origami nanostructures provide a platform where dye molecules can be arranged with nanoscale accuracy allowing to assemble multiple fluorophores without dye-dye aggregation. Aiming to develop a bright and sensitive ratiometric sensor system, we systematically studied the optical properties of nanoarrays of dyes built on DNA origami platforms using a DNA template that provides a high versatility of label choice at minimum cost. The dyes are arranged at distances, at which they efficiently interact by Forster resonance energy transfer (FRET). To optimize array brightness, the FRET efficiencies between the donor fluorescein (FAM) and the acceptor cyanine 3 were determined for different sizes of the array and for different arrangements of the dye molecules within the array. By utilizing nanoarrays providing optimum FRET efficiency and brightness, we subsequently designed a ratiometric pH nanosensor using coumarin 343 as a pH-inert FRET donor and FAM as a pH responsive acceptor. Our results indicate that the sensitivity of a ratiometric sensor can be improved simply by arranging the dyes into a well-defined array. The dyes used here can be easily replaced by other analyte-responsive dyes, demonstrating the huge potential of DNA nanotechnology for light harvesting, signal enhancement, and sensing schemes in life sciences.}, language = {en} } @phdthesis{Olejko2017, author = {Olejko, Lydia}, title = {F{\"o}rster resonance energy transfer (FRET)-based nanophotonics using DNA origami structures}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-396747}, school = {Universit{\"a}t Potsdam}, year = {2017}, abstract = {The field of nanophotonics focuses on the interaction between electromagnetic radiation and matter on the nanometer scale. The elements of nanoscale photonic devices can transfer excitation energy non-radiatively from an excited donor molecule to an acceptor molecule by F{\"o}rster resonance energy transfer (FRET). The efficiency of this energy transfer is highly dependent on the donor-acceptor distance. Hence, in these nanoscale photonic devices it is of high importance to have a good control over the spatial assembly of used fluorophores. Based on molecular self-assembly processes, various nanostructures can be produced. Here, DNA nanotechnology and especially the DNA origami technique are auspicious self-assembling methods. By using DNA origami nanostructures different fluorophores can be introduced with a high local control to create a variety of nanoscale photonic objects. The applications of such nanostructures range from photonic wires and logic gates for molecular computing to artificial light harvesting systems for artificial photosynthesis. In the present cumulative doctoral thesis, different FRET systems on DNA origami structures have been designed and thoroughly analyzed. Firstly, the formation of guanine (G) quadruplex structures from G rich DNA sequences has been studied based on a two-color FRET system (Fluorescein (FAM)/Cyanine3 (Cy3)). Here, the influences of different cations (Na+ and K+), of the DNA origami structure and of the DNA sequence on the G-quadruplex formation have been analyzed. In this study, an ion-selective K+ sensing scheme based on the G-quadruplex formation on DNA origami structures has been developed. Subsequently, the reversibility of the G-quadruplex formation on DNA origami structures has been evaluated. This has been done for the simple two-color FRET system which has then been advanced to a switchable photonic wire by introducing additional fluorophores (FAM/Cy3/Cyanine5 (Cy5)/IRDye®700). In the last part, the emission intensity of the acceptor molecule (Cy5) in a three-color FRET cascade has been tuned by arranging multiple donor (FAM) and transmitter (Cy3) molecules around the central acceptor molecule. In such artificial light harvesting systems, the excitation energy is absorbed by several donor and transmitter molecules followed by an energy transfer to the acceptor leading to a brighter Cy5 emission. Furthermore, the range of possible excitation wavelengths is extended by using several different fluorophores (FAM/Cy3/Cy5). In this part of the thesis, the light harvesting efficiency (antenna effect) and the FRET efficiency of different donor/transmitter/acceptor assemblies have been analyzed and the artificial light harvesting complex has been optimized in this respect.}, language = {en} } @article{WessigBehrendsKumkeetal.2016, author = {Wessig, Pablo and Behrends, Nicole and Kumke, Michael Uwe and Eisold, Ursula}, title = {FRET Pairs with Fixed Relative Orientation of Chromophores}, series = {European journal of organic chemistry}, volume = {145}, journal = {European journal of organic chemistry}, publisher = {Wiley-VCH}, address = {Weinheim}, issn = {1434-193X}, doi = {10.1002/ejoc.201600489}, pages = {4476 -- 4486}, year = {2016}, abstract = {Synthetic routes to different oligospirothioketal (OSTK) Forster resonance energy transfer (FRET) constructs are described and the photophysics of these constructs were explored in different solvents. The FRET efficiencies were determined from the experimental data and compared with theoretical values. The influence of the outstanding rigidity of the novel OSTK compounds on the FRET is discussed.}, language = {en} } @article{CywinskiOlejkoLoehmannsroeben2015, author = {Cywinski, Piotr J. and Olejko, Lydia and L{\"o}hmannsr{\"o}ben, Hans-Gerd}, title = {A time-resolved luminescent competitive assay to detect L-selectin using aptamers as recognition elements}, series = {Analytica chimica acta : an international journal devoted to all branches of analytical chemistry}, volume = {887}, journal = {Analytica chimica acta : an international journal devoted to all branches of analytical chemistry}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0003-2670}, doi = {10.1016/j.aca.2015.06.045}, pages = {209 -- 215}, year = {2015}, abstract = {L-selectin is a protein with potential importance for numerous diseases and clinical disorders. In this paper, we present a new aptamer-based luminescent assay developed to detect L-selectin. The sensing system working principle is based on Forster Resonance Energy Transfer (FRET) from a donor terbium complex (TbC) to an acceptor cyanine dye (Cy5). In the present approach, the biotinylated aptamer is combined with Cy5-labelled streptavidin (Cy5-Strep) to yield an aptamer-based acceptor construct (Apta-Cy5-Strep), while L-selectin is conjugated using luminescent TbC. Upon aptamer binding to the TbC-labelled L-selectin (L-selectin-TbC), permanent donor-acceptor proximity is established which allows for radiationless energy transfer to occur. However, when unlabelled L-selectin is added, it competes with the L-selectin-TbC and the FRET signal decreases as the L-selectin concentration increases. FRET from the TbC to Cy5 was observed with time-gated time-resolved luminescence spectroscopy. A significant change in the corrected luminescence signal was observed in the dynamic range of 10 -500 ng/mL L-selectin, the concentration range relevant for accelerated cognitive decline of Alzheimer's disease, with a limit of detection (LOD) equal to 10 ng/mL. The aptasensor-based assay is homogeneous and can be realized within one hour. Therefore, this method has the potential to become an alternative to tedious heterogeneous analytical methods, e.g. based on enzyme-linked immunosorbent assay (ELISA). (C) 2015 Elsevier B.V. All rights reserved.}, language = {en} } @article{OlejkoCywinskiBald2015, author = {Olejko, Lydia and Cywinski, Piotr J. and Bald, Ilko}, title = {Ion-Selective formation of a guanine quadruplex on DNA origami structures}, series = {Angewandte Chemie : a journal of the Gesellschaft Deutscher Chemiker ; International edition}, volume = {54}, journal = {Angewandte Chemie : a journal of the Gesellschaft Deutscher Chemiker ; International edition}, number = {2}, publisher = {Wiley-VCH}, address = {Weinheim}, issn = {1433-7851}, doi = {10.1002/anie.201409278}, pages = {673 -- 677}, year = {2015}, abstract = {DNA origami nanostructures are a versatile tool that can be used to arrange functionalities with high local control to study molecular processes at a single-molecule level. Here, we demonstrate that DNA origami substrates can be used to suppress the formation of specific guanine (G) quadruplex structures from telomeric DNA. The folding of telomeres into G-quadruplex structures in the presence of monovalent cations (e.g. Na+ and K+) is currently used for the detection of K+ ions, however, with insufficient selectivity towards Na+. By means of FRET between two suitable dyes attached to the 3- and 5-ends of telomeric DNA we demonstrate that the formation of G-quadruplexes on DNA origami templates in the presence of sodium ions is suppressed due to steric hindrance. Hence, telomeric DNA attached to DNA origami structures represents a highly sensitive and selective detection tool for potassium ions even in the presence of high concentrations of sodium ions.}, language = {en} } @article{HildebrandtGeissler2012, author = {Hildebrandt, Niko and Geissler, Daniel}, title = {Semiconductor quantum dots as FRET acceptors for multiplexed diagnostics and molecular ruler application}, series = {Advances in Experimental Medicine and Biology}, volume = {733}, journal = {Advances in Experimental Medicine and Biology}, editor = {Zahavy, E and Ordentlich, A and Yitzhaki, S and Shafferman, A}, publisher = {Springer}, address = {Dordrecht}, isbn = {978-94-007-2554-6}, issn = {0065-2598}, doi = {10.1007/978-94-007-2555-3_8}, pages = {75 -- 86}, year = {2012}, abstract = {Applications based on Forster resonance energy transfer (FRET) play an important role for the determination of concentrations and distances within nanometer-scale systems in vitro and in vivo in many fields of biotechnology. Semiconductor nanocrystals (Quantum dots - QDs) possess ideal properties for their application as FRET acceptors when the donors have long excited state lifetimes and when direct excitation of QDs can be efficiently suppressed. Therefore, luminescent terbium complexes (LTCs) with excited state lifetimes of more than 2 ms are ideal FRET donor candidates for QD-acceptors. This chapter will give a short overview of theoretical and practical background of FRET, QDs and LTCs, and present some recent applications of LTC-QD FRET pairs for multiplexed ultra-sensitive in vitro diagnostics and nanometer-resolution molecular distance measurements.}, language = {en} } @phdthesis{Hildebrandt2006, author = {Hildebrandt, Niko}, title = {Lanthanides and quantum dots : time-resolved laser spectroscopy of biochemical F{\"o}rster Resonance Energy Transfer (FRET) systems}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-12686}, school = {Universit{\"a}t Potsdam}, year = {2006}, abstract = {F{\"o}rster Resonance Energy Transfer (FRET) plays an important role for biochemical applications such as DNA sequencing, intracellular protein-protein interactions, molecular binding studies, in vitro diagnostics and many others. For qualitative and quantitative analysis, FRET systems are usually assembled through molecular recognition of biomolecules conjugated with donor and acceptor luminophores. Lanthanide (Ln) complexes, as well as semiconductor quantum dot nanocrystals (QD), possess unique photophysical properties that make them especially suitable for applied FRET. In this work the possibility of using QD as very efficient FRET acceptors in combination with Ln complexes as donors in biochemical systems is demonstrated. The necessary theoretical and practical background of FRET, Ln complexes, QD and the applied biochemical models is outlined. In addition, scientific as well as commercial applications are presented. FRET can be used to measure structural changes or dynamics at distances ranging from approximately 1 to 10 nm. The very strong and well characterized binding process between streptavidin (Strep) and biotin (Biot) is used as a biomolecular model system. A FRET system is established by Strep conjugation with the Ln complexes and QD biotinylation. Three Ln complexes (one with Tb3+ and two with Eu3+ as central ion) are used as FRET donors. Besides the QD two further acceptors, the luminescent crosslinked protein allophycocyanin (APC) and a commercial fluorescence dye (DY633), are investigated for direct comparison. FRET is demonstrated for all donor-acceptor pairs by acceptor emission sensitization and a more than 1000-fold increase of the luminescence decay time in the case of QD reaching the hundred microsecond regime. Detailed photophysical characterization of donors and acceptors permits analysis of the bioconjugates and calculation of the FRET parameters. Extremely large F{\"o}rster radii of more than 100 {\AA} are achieved for QD as acceptors, considerably larger than for APC and DY633 (ca. 80 and 60 {\AA}). Special attention is paid to interactions with different additives in aqueous solutions, namely borate buffer, bovine serum albumin (BSA), sodium azide and potassium fluoride (KF). A more than 10-fold limit of detection (LOD) decrease compared to the extensively characterized and frequently used donor-acceptor pair of Europium tris(bipyridine) (Eu-TBP) and APC is demonstrated for the FRET system, consisting of the Tb complex and QD. A sub-picomolar LOD for QD is achieved with this system in azide free borate buffer (pH 8.3) containing 2 \% BSA and 0.5 M KF. In order to transfer the Strep-Biot model system to a real-life in vitro diagnostic application, two kinds of imunnoassays are investigated using human chorionic gonadotropin (HCG) as analyte. HCG itself, as well as two monoclonal anti-HCG mouse-IgG (immunoglobulin G) antibodies are labeled with the Tb complex and QD, respectively. Although no sufficient evidence for FRET can be found for a sandwich assay, FRET becomes obvious in a direct HCG-IgG assay showing the feasibility of using the Ln-QD donor-acceptor pair as highly sensitive analytical tool for in vitro diagnostics.}, language = {en} } @misc{BeckHildebrandtLoehmannsroeben2006, author = {Beck, Michael and Hildebrandt, Niko and L{\"o}hmannsr{\"o}ben, Hans-Gerd}, title = {Quantum dots as acceptors in FRET-assays containing serum}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-9504}, year = {2006}, abstract = {Quantum dots (QDs) are common as luminescing markers for imaging in biological applications because their optical properties seem to be inert against their surrounding solvent. This, together with broad and strong absorption bands and intense, sharp tuneable luminescence bands, makes them interesting candidates for methods utilizing F{\"o}rster Resonance Energy Transfer (FRET), e. g. for sensitive homogeneous fluoroimmunoassays (FIA). In this work we demonstrate energy transfer from Eu3+-trisbipyridin (Eu-TBP) donors to CdSe-ZnS-QD acceptors in solutions with and without serum. The QDs are commercially available CdSe-ZnS core-shell particles emitting at 655 nm (QD655). The FRET system was achieved by the binding of the streptavidin conjugated donors with the biotin conjugated acceptors. After excitation of Eu-TBP and as result of the energy transfer, the luminescence of the QD655 acceptors also showed lengthened decay times like the donors. The energy transfer efficiency, as calculated from the decay times of the bound and the unbound components, amounted to 37\%. The F{\"o}rster-radius, estimated from the absorption and emission bands, was ca. 77 {\AA}. The effective binding ratio, which not only depends on the ratio of binding pairs but also on unspecific binding, was obtained from the donor emission dependent on the concentration. As serum promotes unspecific binding, the overall FRET efficiency of the assay was reduced. We conclude that QDs are good substitutes for acceptors in FRET if combined with slow decay donors like Europium. The investigation of the influence of the serum provides guidance towards improving binding properties of QD assays.}, subject = {Quantenpunkt}, language = {en} } @misc{SchulerLipmanSteinbachetal.2005, author = {Schuler, Benjamin and Lipman, Everett A. and Steinbach, Peter J. and Kumke, Michael Uwe and Eaton, William A.}, title = {Polyproline and the "spectroscopic ruler" revisited with single-molecule fluorescence}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-12229}, year = {2005}, abstract = {To determine whether F{\"o}rster resonance energy transfer (FRET) measurements can provide quantitative distance information in single-molecule fluorescence experiments on polypeptides, we measured FRET efficiency distributions for donor and acceptor dyes attached to the ends of freely diffusing polyproline molecules of various lengths. The observed mean FRET efficiencies agree with those determined from ensemble lifetime measurements but differ considerably from the values expected from F{\"o}rster theory, with polyproline treated as a rigid rod. At donor-acceptor distances much less than the F{\"o}rster radius R0, the observed efficiencies are lower than predicted, whereas at distances comparable to and greater than R0, they are much higher. Two possible contributions to the former are incomplete orientational averaging during the donor lifetime and, because of the large size of the dyes, breakdown of the point-dipole approximation assumed in F{\"o}rster theory. End-to-end distance distributions and correlation times obtained from Langevin molecular dynamics simulations suggest that the differences for the longer polyproline peptides can be explained by chain bending, which considerably shortens the donor-acceptor distances.}, language = {en} }