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ResearchZernike (ZIAM)Molecular BiophysicsCordes Group



de Boer, M., Gkouridis, G., Vietrov, R., Begg, S. L., Schuurman-Wolters, G. K., Husada, F., ... Cordes, T. (2019). Conformational and dynamical plasticity in substrate-binding proteins underlies selective transport in ABC importers. eLife, 8, [e44652].
Smit, J. H., van der Velde, J. H. M., Huang, J., Trauschke, V., Henrikus, S. S., Chen, S., ... Cordes, T. (2019). On the impact of competing intra- and intermolecular triplet-state quenching on photobleaching and photoswitching kinetics of organic fluorophores. PPCP : Physical Chemistry Chemical Physics, 21(7), 3721-3733.


Husada, F., Bountra, K., Tassis, K., de Boer, M., Romano, M., Rebuffat, S., ... Cordes, T. (2018). Conformational dynamics of the ABC transporter McjD seen by single-molecule FRET. EMBO Journal, 37(21), [100056].
Hellenkamp, B., Schmid, S., Doroshenko, O., Opanasyuk, O., Kühnemuth, R., Rezaei Adariani, S., ... Hugel, T. (2018). Precision and accuracy of single-molecule FRET measurements-a multi-laboratory benchmark study. Nature Methods, 15(9), 669-676.
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 Forster resonance energy transfer. Science, 359(6373), [1133].


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.


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.
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].
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.
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, 120(26), 6401-6410.
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].


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].
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.
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.
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.


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.
Hohlbein, J., Craggs, T. D., & Cordes, T. (2014). Alternating-laser excitation: single-molecule FRET and beyond. Chemical Society Reviews, 43(4), 1156-1171.
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.


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.
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.
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.
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.


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.
Tinnefeld, P., & Cordes, T. (2012). 'Self-healing' dyes: intramolecular stabilization of organic fluorophores. Nature Methods, 9(5), 426-427.
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.
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.


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.
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.


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.
Vogelsang, J., Cordes, T., Forthmann, C., Steinhauer, C., & Tinnefeld, P. (2010). Intrinsically Resolution Enhancing Probes for Confocal Microscopy. Nano Letters, 10(2), 672-679.
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.
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.
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.
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.


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.
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.
Root, C., Lederer, F. J., Schrader, T. E., Herzog, T. T., Cordes, T., Gilch, P., & Braun, M. (2009). Excitation wavelength dependent pump–probe signatures of molecular crystals. Applied Physics A: Materials Science & Processing, 96(1), 99-106.
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.
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.
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.
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.
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.
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.


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.
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.
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.


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.
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.
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.
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.
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., 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.


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.
Last modified:20 January 2016 12.41 p.m.