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  • Angelin, A.; Kassel, O.; Rastegar, S.; Strähle, U.; Niemeyer, C. M., Protein‐Functionalized DNA Nanostructures as Tools to Control Transcription in Zebrafish Embryos. ChemistryOpen 2017, 6 (1), 33-39. link
  • Bestgen, S.; Seidl, C.; Wiesner, T.; Zimmer, A.; Falk, M.; Köberle, B.; Austeri, M.; Paradies, J.; Bräse, S.; Schepers, U.; Roesky, P. W., Double-Strand DNA Breaks Induced by Paracyclophane Gold(I) Complexes. Chemistry – A European Journal 2017, n/a-n/a. link

  • Heiler, C.; Offenloch, J. T.; Blasco, E.; Barner-Kowollik, C., Photochemically Induced Folding of Single Chain Polymer Nanoparticles in Water. ACS Macro Letters 2016, 56-61. link 

  • Khudoleeva, V. Y.; Utochnikova, V. V.; Kalyakina, A. S.; Deygen, I. M.; Shiryaev, A. A.; Marciniak, Ł.; Lebedev, V. A.; Roslyakov, I. V.; Garshev, A. V.; Lepnev, L. S.; Schepers, U.; Bräse, S.; Kuzmina, N. P., Surface modified EuxLa1-xF3 nanoparticles as luminescent biomarkers: Still plenty of room at the bottom. Dyes and Pigments 2017, 143, 348-355. link

  • Offenloch, J. T.; Willenbacher, J.; Tzvetkova, P.; Heiler, C.; Mutlu, H.; Barner-Kowollik, C., Degradable fluorescent single-chain nanoparticles based on metathesis polymers. Chemical Communications 2017, 53 (4), 775-778. link​​​​​  

  • Steinmeyer, J.; Rönicke, F.; Schepers, U.; Wagenknecht, H.-A., Synthesis of Wavelength-Shifting Fluorescent DNA and RNA with Two Photostable Cyanine–Styryl Dyes as the Base Surrogate Pair. ChemistryOpen, n/a-n/a. link

  • Utochnikova, V. V.; Solodukhin, N. N.; Aslandukov, A. A.; Zaitsev, K. V.; Kalyakina, A. S.; Averin, A. A.; Ananyev, I. A.; Churakov, A. V.; Kuzmina, N. P., Luminescence Enhancement by p-Substituent Variation. European Journal of Inorganic Chemistry 2017, 2017 (1), 107-114. link

  • Walter, H.-K.; Bauer, J.; Steinmeyer, J.; Kuzuya, A.; Niemeyer, C. M.; Wagenknecht, H.-A., “DNA Origami Traffic Lights” with a Split Aptamer Sensor for a Bicolor Fluorescence Readout. Nano Letters 2017. link

  • Walter, H.-K.; Olshausen, B.; Schepers, U.; Wagenknecht, H.-A., A postsynthetically 2’-“clickable” uridine with arabino configuration and its application for fluorescent labeling and imaging of DNA. Beilstein Journal of Organic Chemistry 2017, 13, 127-137. link


  • Altintas, O.; Barner-Kowollik, C., Single-Chain Folding of Synthetic Polymers: A Critical Update. Macromolecular Rapid Communications 2016, 37 (1), 29-46. link
  • Arndt, S.; Walter, H.-K.Wagenknecht, H.-A., Synthesis of Wavelength-shifting DNA Hybridization Probes by Using Photostable Cyanine Dyes. J. Vis. Exp. 2016, 113, e54121. link
  • Ashraf, S.; Park, J.; Bichelberger, M.; Kantner, K.; Hartmann, R.; Maffre, P.; Said, A. H.; Feliu, N.; Lee, J.; Lee, D.; Nienhaus, G. U.; Kim, S.; Parak, W. J., Zwitterionic surface coating of quantum dots reduces protein adsorption and cellular uptake. Nanoscale 2016. link  
  • Babii, O.; Afonin, S.; Garmanchuk, L. V.; Nikulina, V. V.; Nikolaienko, T. V.; Storozhuk, O. V.; Shelest, D. V.; Dasyukevich, O. I.; Ostapchenko, L. I.; Iurchenko, V.; Zozulya, S.; Ulrich, A. S.; Komarov, I. V., Direct Photocontrol of Peptidomimetics: An Alternative to Oxygen-Dependent Photodynamic Cancer Therapy. Angewandte Chemie 2016, 128 (18), 5583-5586.  link
  • Bachollet, S. P. J. T.; Volz, D.; Fiser, B.; Münch, S.Rönicke, F.; Carrillo, J.; Adams, H.; Schepers, U.; Gómez-Bengoa, E.; Bräse, S.; Harrity, J. P. A., A Modular Class of Fluorescent Difluoroboranes: Synthesis, Structure, Optical Properties, Theoretical Calculations and Applications for Biological Imaging. Chemistry – A European Journal 2016, 22 (35), 12430-12438. link
  • Berndl, S.; Dimitrov, S. D.; Menacher, F.; Fiebig, T.; Wagenknecht, H.-A., Thiazole Orange Dimers in DNA: Fluorescent Base Substitutions with Hybridization Readout. Chemistry – A European Journal 2016, n/a-n/a. link  
  • Bohlander, P. R.; Abba, M. L.; Bestvater, F.; Allgayer, H.; Wagenknecht, H.-A., Two wavelength-shifting molecular beacons for simultaneous and selective imaging of vesicular miRNA-21 and miRNA-31 in living cancer cells. Organic & Biomolecular Chemistry 2016, 14 (22), 5001-5006. link
  • Schwechheimer, C.; Merkel, M.; Bohländer, P. R.; Wagenknecht, H.-A., Synthetic Wavelength-Shifting Fluorescent Probes of Nucleic Acids. In Modified Nucleic Acids, Nakatani, K.; Tor, Y., Eds. Springer International Publishing: Cham, 2016; pp 83-100. link
  • Eördögh, Á.; Steinmeyer, J.; Peewasan, K.; Schepers, U.Wagenknecht, H.-A.; Kele, P., Polarity Sensitive Bioorthogonally Applicable Far-Red Emitting Labels for Postsynthetic Nucleic Acid Labeling by Copper-Catalyzed and Copper-Free Cycloaddition. Bioconjugate Chemistry 2016, 27 (2), 457-464. link
  • Gao, P.; Ulrich Nienhaus, G., Confocal laser scanning microscopy with spatiotemporal structured illumination. Opt. Lett. 2016, 41 (6), 1193-1196. link
  • García-Iriepa, C.; Ernst, H. A.; Liang, Y.; Unterreiner, A.-N.; Frutos, L. M.; Sampedro, D., Study of Model Systems for Bilirubin and Bilin Chromophores: Determination and Modification of Thermal and Photochemical Properties. The Journal of Organic Chemistry 2016, 81 (15), 6292-6302. link
  • Geiselhart, C. M.; Offenloch, J. T.; Mutlu, H.; Barner-Kowollik, C., Polybutadiene Functionalization via an Efficient Avenue. ACS Macro Letters 2016, 1146-1151. link 
  • Karin, N.; Nienhaus, G. U., Chromophore photophysics and dynamics in fluorescent proteins of the GFP family. Journal of Physics: Condensed Matter 2016, 28 (44), 443001. link
  • Koehler, C.; Sauter, P. F.; Wawryszyn, M.; Girona, G. E.; Gupta, K.; Landry, J. J. M.; Fritz, M. H.-Y.; Radic, K.; Hoffmann, J.-E.; Chen, Z. A.; Zou, J.; Tan, P. S.; Galik, B.; Junttila, S.; Stolt-Bergner, P.; Pruneri, G.; Gyenesei, A.; Schultz, C.; Biskup, M. B.; Besir, H.; Benes, V.; Rappsilber, J.; Jechlinger, M.; Korbel, J. O.; Berger, I.; Bräse, S.; Lemke, E. A., Genetic code expansion for multiprotein complex engineering. Nat Meth 2016, 13 (12), 997-1000. link
  • Lederhose, P.; Chen, Z.; Müller, R.; Blinco, J. P.; Wu, S.; Barner-Kowollik, C., Near-Infrared Photoinduced Coupling Reactions Assisted by Upconversion Nanoparticles. Angewandte Chemie International Edition 2016, 55 (40), 12195-12199. link
  • Li, Y.; Shang, L.; Nienhaus, G. U., Super-resolution imaging-based single particle tracking reveals dynamics of nanoparticle internalization by live cells. Nanoscale 2016, 8 (14), 7423-7429. link
  • Mende, M.; Bednarek, C.; Wawryszyn, M.; Sauter, P.; Biskup, M. B.; Schepers, U.Bräse, S., Chemical Synthesis of Glycosaminoglycans. Chemical Reviews 2016, 116 (14), 8193-8255. link
  • Merkel, M.; Arndt, S.; Ploschik, D.; Cserép, G. B.; Wenge, U.; Kele, P.; Wagenknecht, H.-A., Scope and Limitations of Typical Copper-Free Bioorthogonal Reactions with DNA: Reactive 2′-Deoxyuridine Triphosphates for Postsynthetic Labeling. The Journal of Organic Chemistry 2016, 81 (17), 7527-7538. link
  • Middel, V.; Zhou, L.; Takamiya, M.; Beil, T.; Shahid, M.; Roostalu, U.; Grabher, C.; Rastegar, S.; Reischl, M.; Nienhaus, G. U.Strähle, U., Dysferlin-mediated phosphatidylserine sorting engages macrophages in sarcolemma repair. Nature communications 2016, 7, 12875. link 
  • Nienhaus, K.; Nienhaus, G. U., Where Do We Stand with Super-Resolution Optical Microscopy, Journal of Molecular Biology 2016, 428 (2, Part A), 308-322. link
  • Pianowski, Z.; Karcher, J.; Schneider, K., Photoresponsive self-healing supramolecular hydrogels for light-induced release of DNA and doxorubicin. Chemical Communications 2016. link
  • Shang, L.; Nienhaus, G. U., Metal nanoclusters: Protein corona formation and implications for biological applications. The International Journal of Biochemistry & Cell Biology 2016, 75, 175-179. link
  • Shang, L.; Yang, L.; Wang, H.; Nienhaus, G. U., In Situ Monitoring of the Intracellular Stability of Nanoparticles by Using Fluorescence Lifetime Imaging. Small 2016, 12 (7), 868-873. link
  • Stockmar, F.; Kobitski, A. Y.; Nienhaus, G. U., Fast Folding Dynamics of an Intermediate State in RNase H Measured by Single-Molecule FRET. The Journal of Physical Chemistry B 2016, 120 (4), 641-649. link
  • Utochnikova, V. V.; Kalyakina, A. S.; Bushmarinov, I. S.; Vashchenko, A. A.; Marciniak, L.; Kaczmarek, A. M.; Van Deun, R.; Bräse, S.; Kuzmina, N. P., Lanthanide 9-anthracenate: solution processable emitters for efficient purely NIR emitting host-free OLEDs. Journal of Materials Chemistry C 2016, 4 (41), 9848-9855. link
  • Wagner, A. T.; Roesky, P. W., Rare-Earth Metal Oxo/Hydroxo Clusters – Synthesis, Structures, and Applications. European Journal of Inorganic Chemistry 2016, 2016 (6), 782-791. link
  • Wang, H.; Shang, L.; Maffre, P.; Hohmann, S.; Kirschhöfer, F.; Brenner-Weiß, G.; Nienhaus, G. U., The Nature of a Hard Protein Corona Forming on Quantum Dots Exposed to Human Blood Serum. Small 2016, n/a-n/a. link 


  • Althuon, D.; Rönicke, F.; Furniss, D.; Quan, J.; Wellhofer, I.; Jung, N.; Schepers, U.Bräse, S., Functionalized triazolopeptoids - a novel class for mitochondrial targeted delivery. Organic & Biomolecular Chemistry 2015, 13 (14), 4226-4230. link
  • Beyer, H. M.; Juillot, S.; Herbst, K.; Samodelov, S. L.; Muller, K.; Schamel, W. W.; Romer, W.; Schafer, E.; Nagy, F.; Strähle, U.; Weber, W.; Zurbriggen, M. D., Red Light-Regulated Reversible Nuclear Localization of Proteins in Mammalian Cells and Zebrafish. ACS synthetic biology 2015, 4 (9), 951-8. link
  • Bohlander, P. R.; Vilaivan, T.; Wagenknecht, H.-A., Strand displacement and duplex invasion into double-stranded DNA by pyrrolidinyl peptide nucleic acids. Organic & Biomolecular Chemistry 2015, 13 (35), 9223-9230. link
  • Diotel, N.; Beil, T.; Strähle, U.; Rastegar, S., Differential expression of id genes and their potential regulator znf238 in zebrafish adult neural progenitor cells and neurons suggests distinct functions in adult neurogenesis. Gene expression patterns : GEP 2015, 19 (1-2), 1-13. link 
  • Diotel, N.; Rodriguez Viales, R.; Armant, O.; Marz, M.; Ferg, M.; Rastegar, S.; Strähle, U., Comprehensive expression map of transcription regulators in the adult zebrafish telencephalon reveals distinct neurogenic niches. The Journal of comparative neurology 2015, 523 (8), 1202-21. link
  • Guo, Y.; Wolter, T.; Kubař, T.; Sumser, M.; Trauner, D.; Elstner, M., Molecular Dynamics Investigation of gluazo, a Photo-Switchable Ligand for the Glutamate Receptor GluK2. PloS one 2015, 10 (8), e0135399. link
  • Hausen, J.; Otte, J. C.; Strähle, U.; Hammers-Wirtz, M.; Hollert, H.; Keiter, S. H.; Ottermanns, R., Fold-change threshold screening: a robust algorithm to unmask hidden gene expression patterns in noisy aggregated transcriptome data. Environmental science and pollution research international 2015, 22 (21), 16384-92. link
  • Hense, A.; Prunsche, B.; Gao, P.; Ishitsuka, Y.; Nienhaus, K.; Ulrich Nienhaus, G., Monomeric Garnet, a far-red fluorescent protein for live-cell STED imaging. Scientific reports 2015, 5, 18006. link
  • Hörner, A.; Hagendorn, T.; Schepers, U.Bräse, S., Photophysical Properties and Synthesis of New Dye–Cyclooctyne Conjugates for Multicolor and Advanced Microscopy. Bioconjugate Chemistry 2015, 26 (4), 718-724. link
  • Ishitsuka, Y.; Azadfar, N.; Kobitski, A. Y.; Nienhaus, K.; Johnsson, N.; Nienhaus, G. U., Evaluation of Genetically Encoded Chemical Tags as Orthogonal Fluorophore Labeling Tools for Single-Molecule FRET Applications. The Journal of Physical Chemistry B 2015, 119 (22), 6611-6619. link
  • Kalyakina, A. S.; Utochnikova, V. V.; Bushmarinov, I. S.; Ananyev, I. V.; Eremenko, I. L.; Volz, D.; Rönicke, F.Schepers, U.; Van Deun, R.; Trigub, A. L.; Zubavichus, Y. V.; Kuzmina, N. P.; Bräse, S., Highly Luminescent, Water-Soluble Lanthanide Fluorobenzoates: Syntheses, Structures and Photophysics, Part I: Lanthanide Pentafluorobenzoates. Chemistry – A European Journal 2015, 21 (49), 17921-17932. link
  • Klapper, Y.; Maffre, P.; Shang, L.; Ekdahl, K. N.; Nilsson, B.; Hettler, S.; Dries, M.; Gerthsen, D.; Nienhaus, G. U., Low affinity binding of plasma proteins to lipid-coated quantum dots as observed by in situ fluorescence correlation spectroscopy. Nanoscale 2015, 7 (22), 9980-9984. link 
  • Kobitski, A. Y.; Otte, J. C.; Takamiya, M.; Schafer, B.; Mertes, J.; Stegmaier, J.; Rastegar, S.; Rindone, F.; Hartmann, V.; Stotzka, R.; Garcia, A.; van Wezel, J.; Mikut, R.; Strähle, U.Nienhaus, G. U., An ensemble-averaged, cell density-based digital model of zebrafish embryo development derived from light-sheet microscopy data with single-cell resolution. Scientific reports 2015, 5, 8601. link
  • Marcato, D.; Alshut, R.; Breitwieser, H.; Mikut, R.; Strähle, U.; Pylatiuk, C.; Peravali, R. In An automated and high-throughput Photomotor Response platform for chemical screens, Engineering in Medicine and Biology Society (EMBC), 2015 37th Annual International Conference of the IEEE, 25-29 Aug. 2015; 2015; pp 7728-7731. link      
  • Merkel, M.; Peewasan, K.; Arndt, S.; Ploschik, D.; Wagenknecht, H.-A., Copper-Free Postsynthetic Labeling of Nucleic Acids by Means of Bioorthogonal Reactions. ChemBioChem 2015, 16 (11), 1541-1553. link                     
  • Naville, M.; Ishibashi, M.; Ferg, M.; Bengani, H.; Rinkwitz, S.; Krecsmarik, M.; Hawkins, T. A.; Wilson, S. W.; Manning, E.; Chilamakuri, C. S.; Wilson, D. I.; Louis, A.; Lucy Raymond, F.; Rastegar, S.; Strähle, U.; Lenhard, B.; Bally-Cuif, L.; van Heyningen, V.; FitzPatrick, D. R.; Becker, T. S.; Roest Crollius, H., Long-range evolutionary constraints reveal cis-regulatory interactions on the human X chromosome. Nature communications 2015, 6, 6904. link
  • Pelaz, B.; del Pino, P.; Maffre, P.; Hartmann, R.; Gallego, M.; Rivera-Fernández, S.; de la Fuente, J. M.; Nienhaus, G. U.; Parak, W. J., Surface Functionalization of Nanoparticles with Polyethylene Glycol: Effects on Protein Adsorption and Cellular Uptake. ACS Nano 2015, 9 (7), 6996-7008. link
  • Scheidecker, S.; Etard, C.; Haren, L.; Stoetzel, C.; Hull, S.; Arno, G.; Plagnol, V.; Drunat, S.; Passemard, S.; Toutain, A.; Obringer, C.; Koob, M.; Geoffroy, V.; Marion, V.; Strähle, U.; Ostergaard, P.; Verloes, A.; Merdes, A.; Moore, A. T.; Dollfus, H., Mutations in TUBGCP4 alter microtubule organization via the gamma-tubulin ring complex in autosomal-recessive microcephaly with chorioretinopathy. American journal of human genetics 2015, 96 (4), 666-74. link  
  • Takamiya, M.; Weger, B. D.; Schindler, S.; Beil, T.; Yang, L.; Armant, O.; Ferg, M.; Schlunck, G.; Reinhard, T.; Dickmeis, T.; Rastegar, S.; Strähle, U., Molecular description of eye defects in the zebrafish Pax6b mutant, sunrise, reveals a Pax6b-dependent genetic network in the developing anterior chamber. PloS one 2015, 10 (2), e0117645. link
  • Thielemann, D. T.; Wagner, A. T.; Lan, Y.; Oña-Burgos, P.; Fernández , I.; Rösch , E. S.; Kölmel, D. K.; Powell , A. K.; Bräse , S.Roesky, P. W., Peptoid-Ligated Pentadecanuclear Yttrium and Dysprosium Hydroxy Clusters. Chemistry – A European Journal 2015, 21 (7), 2813-2820. link
  • Viales, R. R.; Diotel, N.; Ferg, M.; Armant, O.; Eich, J.; Alunni, A.; Marz, M.; Bally-Cuif, L.; Rastegar, S.; Strähle, U., The helix-loop-helix protein id1 controls stem cell proliferation during regenerative neurogenesis in the adult zebrafish telencephalon. Stem cells (Dayton, Ohio) 2015, 33 (3), 892-903. link
  • Vogt, A.; Guo, Y.; Tsunoda, S. P.; Kateriya, S.; Elstner, M.; Hegemann, P., Conversion of a light-driven proton pump into a light-gated ion channel. Scientific reports 2015, 5. link
  • Walter, H.-K.; Bohländer, P. R.; Wagenknecht, H.-A., Development of a Wavelength-Shifting Fluorescent Module for the Adenosine Aptamer Using Photostable Cyanine Dyes. ChemistryOpen 2015, 4 (2), 92-96. link
  • Wang, X.-D.; Rabe, K. S.; Ahmed, I.; Niemeyer, C. M., Multifunctional Silica Nanoparticles for Covalent Immobilization of Highly Sensitive Proteins. Advanced Materials 2015, 27 (48), 7945-7950. link



Horner, A.; Volz, D.; Hagendorn, T.; Furniss, D.; Greb, L.; Rönicke, F.; Nieger, M.; Schepers, U.Bräse, S., Switchable fluorescence by click reaction of a novel azidocarbazole dye. RSC Advances 2014, 4 (23), 11528-11534. link

Kölmel, D. K.; Hörner, A.; Rönicke, F.; Nieger, M.; Schepers, U.Bräse, S., Cell-penetrating peptoids: Introduction of novel cationic side chains. European Journal of Medicinal Chemistry 2014, 79, 231-243. 3. link 

Wallesch, M.; Volz, D.; Zink, D. M.; Schepers, U.; Nieger, M.; Baumann, T.; Bräse, S., Bright Coppertunities: Multinuclear CuI Complexes with N–P Ligands and Their Applications. Chemistry – A European Journal 2014, 20 (22), 6578-6590. link       

Walther, T. H.; Ulrich, A. S., Transmembrane helix assembly and the role of salt bridges. Curr Opin Struc Biol 2014, 27, 63-68. link

Willenbacher, J.; Wuest, K. N. R.; Mueller, J. O.; Kaupp, M.; Wagenknecht, H.-A.Barner-Kowollik, C., Photochemical Design of Functional Fluorescent Single-Chain Nanoparticles. ACS Macro Letters 2014, 3 (6), 574-579. 2015 link