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OnderzoekZernike (ZIAM)MBPCordes Group



Herten, D-P., Brox, D., Haderspeck, A., & Cordes, T. M. (2018). Synthesis and structure of chemically switchable fluorescent probes on the basis of amino acids (Patent No. WO2018068893.)
Lerner, E., Cordes, T., Ingargiola, A., Alhadid, Y., Chung, S., Michalet, X., & Weiss, S. (2018). Toward dynamic structural biology: Two decades of single-molecule Förster resonance energy transfer. Science, 359(6373). DOI: 10.1126/science.aan1133


Robb, N. C., te Velthuis, A. J. W., Wieneke, R., Tampe, R., Cordes, T., Fodor, E., & Kapanidis, A. N. (2016). Single-molecule FRET reveals the pre-initiation and initiation conformations of influenza virus promoter RNA. Nucleic Acids Research, 44(21), 10304-10315. DOI: 10.1093/nar/gkw884
Ploetz, E., Lerner, E., Husada, F., Roelfs, M., Chung, S., Hohlbein, J., ... Cordes, T. (2016). Forster resonance energy transfer and protein-induced fluorescence enhancement as synergetic multiscale molecular rulers. Scientific Reports, 6, [33257]. DOI: 10.1038/srep33257
Kitzig, S., Thilemann, M., Cordes, T., & Rueck-Braun, K. (2016). Light-Switchable Peptides with a Hemithioindigo Unit: Peptide Design, Photochromism, and Optical Spectroscopy. Chemphyschem, 17(9), 1252-1263. DOI: 10.1002/cphc.201501050
van der Velde, J. H. M., Oelerich, J., Huang, J., Smit, J. H., Aminian Jazi, A., Galiani, S., ... Cordes, T. (2016). A simple and versatile design concept for fluorophore derivatives with intramolecular photostabilization. Nature Communications, 7, [10144]. DOI: 10.1038/ncomms10144
Lerner, E., Ploetz, E., Hohlbein, J., Cordes, T., & Weiss, S. (2016). A Quantitative Theoretical Framework For Protein-Induced Fluorescence Enhancement-Förster-Type Resonance Energy Transfer (PIFE-FRET). The Journal of Physical Chemistry. B: Materials, Surfaces, Interfaces, & Biophysical. DOI: 10.1021/acs.jpcb.6b03692


Jazi, A. A., Ploetz, E., Arizki, M., Dhandayuthapani, B., Waclawska, I., Krämer, R., ... Cordes, T. (2017). Caging and Photoactivation in Single-Molecule Forster Resonance Energy Transfer Experiments. Biochemistry, 56(14), 2031-2041. DOI: 10.1021/acs.biochem.6b00916


Hell, S. W., Sahl, S. J., Bates, M., Zhuang, X., Heintzmann, R., Booth, M. J., ... Cordes, T. (2015). The 2015 super-resolution microscopy roadmap. Journal of Physics D-Applied Physics, 48(44), [443001]. DOI: 10.1088/0022-3727/48/44/443001
Gouridis, G., Schuurman-Wolters, G., Ploetz, E., Husada, F., Vietrov, R., de Boer, M., ... Poolman, B. (2015). Conformational dynamics in substrate-binding domains influences transport in the ABC importer GlnPQ. Nature Structural & Molecular Biology, 22(1), 57-64. DOI: 10.1038/nsmb.2929
van der Velde, J. H. M., Uusitalo, J. J., Ugen, L-J., Warszawik, E. M., Herrmann, A., Marrink, S. J., & Cordes, T. (2015). Intramolecular photostabilization via triplet-state quenching: design principles to make organic fluorophores "self-healing". Faraday Discussions. DOI: 10.1039/c5fd00114e
Husada, F., Gouridis, G., Vietrov, R., Schuurman-Wolters, G. K., Ploetz, E., de Boer, M., ... Cordes, T. (2015). Watching conformational dynamics of ABC transporters with single-molecule tools. Biochemical Society Transactions, 43(5), 1041-1047. DOI: 10.1042/BST20150140


van der Velde, J. H. M., Oelerich, J., Huang, J., Smit, J. H., Hiermaier, M., Ploetz, E., ... Cordes, T. (2014). The Power of Two: Covalent Coupling of Photostabilizers for Fluorescence Applications. The Journal of Physical Chemistry Letters, 5(21), 3792-3798. DOI: 10.1021/jz501874f
Hohlbein, J., Craggs, T. D., & Cordes, T. (2014). Alternating-laser excitation: single-molecule FRET and beyond. Chemical Society Reviews, 43(4), 1156-1171. DOI: 10.1039/c3cs60233h
Ploetz, E., Visser, B., Slingenbergh, W., Evers, K., Martinez-Martinez, D., Pei, Y. T., ... van Dorp, W. F. (2014). Selective functionalization of patterned glass surfaces. Journal of materials chemistry b, 2(17), 2606-2615. DOI: 10.1039/c3tb21763a


van der Velde, J. H. M., Ploetz, E., Hiermaier, M., Oelerich, J., de Vries, J., Roelfes, J., & Cordes, T. (2013). Mechanism of Intramolecular Photostabilization in Self-Healing Cyanine Fluorophores. Chemphyschem, 14(18), 4084-4093. DOI: 10.1002/cphc.201300785
Cordes, T., & Blum, S. A. (2013). Opportunities and challenges in single-molecule and single-particle fluorescence microscopy for mechanistic studies of chemical reactions. Nature Chemistry, 5(12), 993-999. DOI: 10.1038/NCHEM.1800
Robb, N. C., Cordes, T., Hwang, L. C., Gryte, K., Duchi, D., Craggs, T. D., ... Kapanidis, A. N. (2013). The Transcription Bubble of the RNA Polymerase-Promoter Open Complex Exhibits Conformational Heterogeneity and Millisecond-Scale Dynamics: Implications for Transcription Start-Site Selection. Journal of Molecular Biology, 425(5), 875-885. DOI: 10.1016/j.jmb.2012.12.015
Herzog, T. T., Ryseck, G., Ploetz, E., & Cordes, T. (2013). The photochemical ring opening reaction of chromene as seen by transient absorption and fluorescence spectroscopy. Photochemical & Photobiological Sciences, 12(7), 1202-1209. DOI: 10.1039/c3pp50020a


Slingenbergh, W., Boer, S. K. D., Cordes, T., Browne, W. R., Feringa, B. L., Hoogenboom, J. P., ... Dorp, W. F. V. (2012). Selective Functionalization of Tailored Nanostructures. Acs Nano, 6(10), 9214-9220. DOI: 10.1021/nn303571p
Tinnefeld, P., & Cordes, T. (2012). 'Self-healing' dyes: intramolecular stabilization of organic fluorophores. Nature Methods, 9(5), 426-427. DOI: 10.1038/nmeth.1977
Regner, N., Herzog, T. T., Haiser, K., Hoppmann, C., Beyermann, M., Sauermann, J., ... Rück-Braun, K. (2012). Light-Switchable Hemithioindigo-Hemistilbene-Containing Peptides: Ultrafast Spectroscopy of the Z -> E Isomerization of the Chromophore and the Structural Dynamics of the Peptide Moiety. Journal of Physical Chemistry B, 116(14), 4181-4191. DOI: 10.1021/jp300982a
Stein, I. H., Capone, S., Smit, J. H., Baumann, F., Cordes, T., & Tinnefeld, P. (2012). Linking Single-Molecule Blinking to Chromophore Structure and Redox Potentials. Chemphyschem, 13(4), 931-937. DOI: 10.1002/cphc.201100820


Schrader, T. E., Cordes, T., Schreier, W. J., Koller, F. O., Dong, S-L., Moroder, L., & Zinth, W. (2011). Folding and Unfolding of Light-Triggered beta-Hairpin Model Peptides. The Journal of Physical Chemistry B, 115(18), 5219-5226. DOI: 10.1021/jp107683d
Cordes, T., Maiser, A., Steinhauer, C., Schermelleh, L., & Tinnefeld, P. (2011). Mechanisms and advancement of antifading agents for fluorescence microscopy and single-molecule spectroscopy. Physical Chemistry Chemical Physics, 13(14), 6699-6709. DOI: 10.1039/c0cp01919d


Cordes, T., Vogelsang, J., Anaya, M., Spagnuolo, C., Gietl, A., Summerer, W., ... Müllen, K. (2010). Single-Molecule Redox Blinking of Perylene Diimide Derivatives in Water. Journal of the American Chemical Society, 132(7), 2404-2409. DOI: 10.1021/ja9099714
Vogelsang, J., Cordes, T., Forthmann, C., Steinhauer, C., & Tinnefeld, P. (2010). Intrinsically Resolution Enhancing Probes for Confocal Microscopy. Nano Letters, 10(2), 672-679. DOI: 10.1021/nl903823s
Cordes, T., Strackharn, M., Stahl, S. W., Summerer, W., Steinhauer, C., Forthmann, C., ... Tinnefeld, P. (2010). Resolving Single-Molecule Assembled Patterns with Superresolution Blink-Microscopy. Nano Letters, 10(2), 645-651. DOI: 10.1021/nl903730r
Vogelsang, J., Steinhauer, C., Forthmann, C., Stein, I. H., Person-Skegro, B., Cordes, T., & Tinnefeld, P. (2010). Make them Blink: Probes for Super-Resolution Microscopy. Chemphyschem, 11(12), 2475-2490. DOI: 10.1002/cphc.201000189
Cordes, T., Santoso, Y., Tomescu, A. I., Gryte, K., Hwang, L. C., Camará, B., ... Kapanidis, A. N. (2010). Sensing DNA Opening in Transcription Using Quenchable Förster Resonance Energy Transfer. Biochemistry, 49(43), 9171-9180. DOI: 10.1021/bi101184g
Nenov, A., Cordes, T., Herzog, T. T., Zinth, W., & Vivie-Riedle, R. D. (2010). Molecular Driving Forces for Z/E Isomerization Mediated by Heteroatoms: The Example Hemithioindigo. The Journal of Physical Chemistry. A: Molecules, Spectroscopy, Kinetics, Environment, & General Theory, 114(50), 13016-13030. DOI: 10.1021/jp107899g


Böttcher, C., Zeyat, G., Ahmed, S. A., Irran, E., Cordes, T., Elsner, C., ... Rueck-Braun, K. (2009). Synthesis of novel photochromic pyrans via palladium-mediated reactions. Beilstein Journal of Organic Chemistry, 5(25), 1-7. DOI: 10.3762/bjoc.5.25
Cordes, T., Regner, N., Heinz, B., Borysova, E., Ryseck, G., & Gilch, P. (2009). The complex photo-rearrangement of a heterocyclic N-oxide: Kinetics from picoseconds to minutes. Journal of Photochemistry and Photobiology A: Chemistry, 206(1), 10-17. DOI: 10.1016/j.jphotochem.2009.05.015
Vogelsang, J., Cordes, T., Forthmann, C., Steinhauer, C., & Tinnefeld, P. (2009). Controlling the fluorescence of ordinary oxazine dyes for single-molecule switching and superresolution microscopy. Proceedings of the National Academy of Sciences of the United States of America, 106(20), 8107-8112. DOI: 10.1073/pnas.0811875106
Root, C., Lederer, F. J., Schrader, T. E., Herzog, T. T., Cordes, T., Gilch, P., ... Elsässer, T. (Ed.) (2009). Excitation wavelength dependent pump–probe signatures of molecular crystals. Applied Physics A: Materials Science & Processing, 96(1), 99-106. DOI: 10.1007/s00339-009-5169-3
Elsner, C., Cordes, T., Dietrich, P., Zastrow, M., Herzog, T. T., Rück-Braun, K., & Zinth, W. (2009). Photochromic Bis(thiophen-3-yl)maleimides Studied with Time-Resolved Spectroscopy. The Journal of Physical Chemistry. A: Molecules, Spectroscopy, Kinetics, Environment, & General Theory, 113(6), 1033-1039. DOI: 10.1021/jp806945m
Vogelsang, J., Cordes, T., & Tinnefeld, P. (2009). Single-molecule photophysics of oxazines on DNA and its application in a FRET switch. Photochemical & Photobiological Sciences, 8(4), 486-496. DOI: 10.1039/b822318c
Cordes, T., Herzog, T. T., Malkmus, S., Draxler, S., Brust, T., DiGirolamo, J. A., ... Braun, M. (2009). Wavelength and solvent independent photochemistry: the electrocyclic ring-closure of indolylfulgides. Photochemical & Photobiological Sciences, 8(4), 528-534. DOI: 10.1039/b817627b
Cordes, T., Vogelsang, J., & Tinnefeld, P. (2009). On the Mechanism of Trolox as Antiblinking and Antibleaching Reagent. Journal of the American Chemical Society, 131(14), 5018-5019. DOI: 10.1021/ja809117z
Cordes, T., Elsner, C., Herzog, T. T., Hoppmann, C., Schadendorf, T., Summerer, W., ... Zinth, W. (2009). Ultrafast Hemithioindigo-based peptide-switches. Chemical Physics, 358(1), 103-110. DOI: 10.1016/j.chemphys.2008.12.027


Cordes, T., Malkmus, S., DiGirolamo, J. A., Lees, W. J., Nenov, A., Vivie-Riedle, R. D., ... Zinth, W. (2008). Accelerated and Efficient Photochemistry from Higher Excited Electronic States in Fulgide Molecules. The Journal of Physical Chemistry. A: Molecules, Spectroscopy, Kinetics, Environment, & General Theory, 112(51), 13364-13371. DOI: 10.1021/jp807097w
Cordes, T., Schadendorf, T., Priewisch, B., Rück-Braun, K., & Zinth, W. (2008). The Hammett Relationship and Reactions in the Excited Electronic State: Hemithioindigo Z/E-Photoisomerization. The Journal of Physical Chemistry. A: Molecules, Spectroscopy, Kinetics, Environment, & General Theory, 112(4), 581-588. DOI: 10.1021/jp077472l
Cordes, T., Schadendorf, T., Rück-Braun, K., & Zinth, W. (2008). Chemical control of Hemithioindigo-photoisomerization – Substituent-effects on different molecular parts. Chemical Physics Letters, 455(4), 197-201. DOI: 10.1016/j.cplett.2008.02.096


Koller, F. O., Sobotta, C., Schrader, T. E., Cordes, T., Schreier, W. J., Sieg, A., & Gilch, P. (2007). Slower processes of the ultrafast photo-isomerization of an azobenzene observed by IR spectroscopy. Chemical Physics, 341(1), 258-266. DOI: 10.1016/j.chemphys.2007.06.048
Zinth, W., Schrader, T. E., Schreier, W. J., Koller, F. O., Cordes, T., Babitzki, G., ... Renner, C. (2007). Ultrafast Unzipping of a Beta-Hairpin Peptide. In P. Corkum, D. M. Jonas, R. J. D. Miller, & A. M. Weiner (Eds.), Ultrafast Phenomena XV (88 ed., pp. 498-500). Berlin, Heidelberg, New York: University of Groningen, The Zernike Institute for Advanced Materials.
Cordes, T., Riesselmann, K., Herre, S., Rück-Braun, K., & Zinth, W. (2007). A New Class of Ultrafast Photoswitchable Chromopeptides. In P. Corkum, D. M. Jonas, R. J. D. Miller, & A. M. Weiner (Eds.), Ultrafast Phenomena XV (88 ed., pp. 543-545). Berlin, Heidelberg, New York: University of Groningen, The Zernike Institute for Advanced Materials.
Cordes, T., Heinz, B., Regner, N., Hoppmann, C., Schrader, T. E., Summerer, W., ... Zinth, W. (2007). Photochemical Z→E Isomerization of a Hemithioindigo/Hemistilbene ω-Amino Acid. Chemphyschem, 8(11), 1713-1721. DOI: 10.1002/cphc.200700223
Schrader, T. E., Schreier, W. J., Cordes, T., Koller, F. O., Babitzki, G., Denschlag, R., ... Zinth, W. (2007). Light-triggered β-hairpin folding and unfolding. Proceedings of the National Academy of Sciences of the United States of America, 104(40), 15729-15734. DOI: 10.1073pnas.0707322104


Cordes, T., Weinrich, D., Kempa, S., Riesselmann, K., Herre, S., Hoppmann, C., ... Zinth, W. (2006). Hemithioindigo-based photoswitches as ultrafast light trigger in chromopeptides. Chemical Physics Letters, 428(1), 167-173. DOI: 10.1016/j.cplett.2006.07.043


Baars-Hibbe, L., Schrader, C., Sichler, P., Cordes, T., Gericke, K-H., Büttgenbach, S., & Draeger, S. (2004). Micro-structured electrode arrays: high-frequency discharges at atmospheric pressure—characterization and new applications. Vacuum, 73(3), 327-332. DOI: 10.1016/j.vacuum.2003.12.107
Last modified:20 January 2016 12.41 p.m.