Publications
2021
Plötz,
E., Schuurman-Wolters, G., Zijlstra, N., Jager, A.,
Griffith, D., Guskov, A., Gouridis, G., Poolman,
B., & Cordes, T. (2021). Structural
and biophysical characterization of the tandem substrate-binding
domains of the ABC importer GlnPQ. Open
Biology, 11(4), [200406]. https://doi.org/10.1098/rsob.200406
Gouridis,
G., Muthahari, Y. A., de Boer, M., Griffith, D. A.,
Tsirigotaki, A., Tassis, K., Zijlstra, N., Xu, R.,
Eleftheriadis, N., Sugijo, Y., Zacharias, M., Domling,
A., Karamanou, S., Pozidis, C., Economou, A., &
Cordes, T. (2021). Structural dynamics in the
evolution of a bilobed protein scaffold.
Proceedings of the National Academy of Sciences of the
United States of America, 118(49),
[e2026165118]. https://doi.org/10.1073/pnas.2026165118
2020
de
Boer, M., Cordes, T., & Poolman,
B. (2020). Kinetic Modelling of Transport Inhibition
by Substrates in ABC Importers. Journal of
Molecular Biology, 432(20), 5565-5576. https://doi.org/10.1016/j.jmb.2020.08.008
2019
Gouridis,
G., Hetzert, B., Kiosze-Becker, K., de Boer, M.,
Heinemann, H., Nuerenberg-Goloub, E., Cordes, T.,
& Tampe, R. (2019). ABCE1 Controls Ribosome Recycling by
an Asymmetric Dynamic Conformational Equilibrium.
Cell reports, 28(3), 723-734.e6. https://doi.org/10.1016/j.celrep.2019.06.052
Smit,
J. H., Li, Y., Warszawik, E. M., Herrmann,
A., & Cordes, T. (2019). ColiCoords:
A Python package for the analysis of bacterial fluorescence
microscopy data. PLoS ONE,
14(6), [0217524]. https://doi.org/10.1371/journal.pone.0217524
de
Boer, M., Gkouridis, G., Vietrov, R., Begg, S. L.,
Schuurman-Wolters, G. K., Husada, F., Eleftheriadis, N.,
Poolman, B., McDevitt, C. A., & Cordes, T.
(2019). Conformational and dynamical plasticity in
substrate-binding proteins underlies selective transport in ABC
importers. eLife, 8,
[e44652]. https://doi.org/10.7554/eLife.44652
Smit,
J. H., van der Velde, J. H. M., Huang,
J., Trauschke, V., Henrikus, S. S., Chen, S.,
Eleftheriadis, N., Warszawik, E. M., Herrmann,
A., & 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. https://doi.org/10.1039/c8cp05063e
van
der Velde, J. H. M., Smit, J. H., Hebisch, E., Punter,
M., & Cordes, T. (2019). Self-healing
dyes for super-resolution fluorescence microscopy.
Journal of Physics D-Applied Physics,
52(3), [034001]. https://doi.org/10.1088/1361-6463/aae752
de
Boer, M., Gouridis, G., Muthahari, Y. A., &
Cordes, T. (2019). Single-Molecule Observation of
Ligand Binding and Conformational Changes in FeuA.
Biophysical Journal, 117(9),
1642-1654. https://doi.org/10.1016/j.bpj.2019.08.005
2018
Husada,
F., Bountra, K., Tassis, K., de Boer, M.,
Romano, M., Rebuffat, S., Beis, K., & Cordes, T.
(2018). Conformational dynamics of the ABC transporter McjD
seen by single-molecule FRET. EMBO
Journal, 37(21), [100056]. https://doi.org/10.15252/embj.2018100056
Hellenkamp,
B., Schmid, S., Doroshenko, O., Opanasyuk, O., Kühnemuth, R.,
Rezaei Adariani, S., Ambrose, B., Aznauryan, M., Barth, A.,
Birkedal, V., Bowen, M. E., Chen, H., Cordes, T.,
Eilert, T., Fijen, C., Gebhardt, C., Götz, M., Gouridis, G.,
Gratton, E., ... Hugel, T. (2018). Precision and accuracy of
single-molecule FRET measurements-a multi-laboratory benchmark
study. Nature Methods, 15(9),
669-676. https://doi.org/10.1038/s41592-018-0085-0
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). https://worldwide.espacenet.com/publicationDetails/originalDocument?CC=WO&NR=2018068893A1&KC=A1&FT=D&ND=3&date=20180419&DB=&locale=en_EP
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]. https://doi.org/10.1126/science.aan1133
2017
Jazi,
A. A., Ploetz, E., Arizki, M., Dhandayuthapani, B., Waclawska, I.,
Krämer, R., Ziegler, C., & Cordes, T. (2017).
Caging and Photoactivation in Single-Molecule Forster
Resonance Energy Transfer Experiments.
Biochemistry, 56(14), 2031-2041. https://doi.org/10.1021/acs.biochem.6b00916
2016
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. https://doi.org/10.1021/acs.jpcb.6b03692
van
der Velde, J. H. M., Oelerich, J., Huang, J.,
Smit, J. H., Aminian Jazi, A., Galiani, S., Kolmakov, K., Guoridis,
G., Eggeling, C., Herrmann, A., Roelfes,
G., & Cordes, T. (2016). A simple and
versatile design concept for fluorophore derivatives with
intramolecular photostabilization. Nature
Communications, 7, [10144]. https://doi.org/10.1038/ncomms10144
Ploetz,
E., Lerner, E., Husada, F., Roelfs, M., Chung, S., Hohlbein, J.,
Weiss, S., & Cordes, T. (2016). Forster
resonance energy transfer and protein-induced fluorescence
enhancement as synergetic multiscale molecular rulers.
Scientific Reports, 6, [33257]. https://doi.org/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. https://doi.org/10.1002/cphc.201501050
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. https://doi.org/10.1093/nar/gkw884
2015
Gouridis,
G., Schuurman-Wolters, G., Ploetz, E., Husada, F.,
Vietrov, R., de Boer, M., Cordes,
T., & Poolman, B. (2015).
Conformational dynamics in substrate-binding domains
influences transport in the ABC importer GlnPQ.
Nature Structural & Molecular Biology,
22(1), 57-64. https://doi.org/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.
https://doi.org/10.1039/c5fd00114e
Hell,
S. W., Sahl, S. J., Bates, M., Zhuang, X., Heintzmann, R., Booth,
M. J., Bewersdorf, J., Shtengel, G., Hess, H., Tinnefeld, P.,
Honigmann, A., Jakobs, S., Testa, I., Cognet, L., Lounis, B.,
Ewers, H., Davis, S. J., Eggeling, C., Klenerman, D., ...
Cordes, T. (2015). The 2015 super-resolution
microscopy roadmap. Journal of Physics D-Applied
Physics, 48(44), [443001]. https://doi.org/10.1088/0022-3727/48/44/443001
Husada,
F., Gouridis, G., Vietrov, R., Schuurman-Wolters, G.
K., Ploetz, E., de Boer, M., Poolman,
B., & Cordes, T. (2015). Watching
conformational dynamics of ABC transporters with single-molecule
tools. Biochemical Society
Transactions, 43(5), 1041-1047. https://doi.org/10.1042/BST20150140
2014
Hohlbein,
J., Craggs, T. D., & Cordes, T. (2014).
Alternating-laser excitation: single-molecule FRET and
beyond. Chemical Society Reviews,
43(4), 1156-1171. https://doi.org/10.1039/c3cs60233h
Ploetz,
E., Visser, B., Slingenbergh, W., Evers, K., Martinez-Martinez,
D., Pei, Y. T., Feringa, B. L., De
Hosson, J. T. M., Cordes, T., & van Dorp,
W. F. (2014). Selective functionalization of patterned glass
surfaces. Journal of materials chemistry
b, 2(17), 2606-2615. https://doi.org/10.1039/c3tb21763a
van
der Velde, J. H. M., Oelerich, J., Huang, J.,
Smit, J. H., Hiermaier, M., Ploetz, E., Herrmann,
A., Roelfes, G., & Cordes, T.
(2014). The Power of Two: Covalent Coupling of
Photostabilizers for Fluorescence Applications.
The Journal of Physical Chemistry Letters,
5(21), 3792-3798. https://doi.org/10.1021/jz501874f
2013
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. https://doi.org/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. https://doi.org/10.1038/NCHEM.1800
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. https://doi.org/10.1039/c3pp50020a
Robb,
N. C., Cordes, T., Hwang, L. C., Gryte, K., Duchi, D.,
Craggs, T. D., Santoso, Y., Weiss, S., Ebright, R. H., &
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. https://doi.org/10.1016/j.jmb.2012.12.015
2012
Regner,
N., Herzog, T. T., Haiser, K., Hoppmann, C., Beyermann, M.,
Sauermann, J., Engelhard, M., Cordes, T., Rueck-Braun,
K., Zinth, W., & 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. https://doi.org/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. https://doi.org/10.1002/cphc.201100820
Slingenbergh,
W., Boer, S. K. D., Cordes, T., Browne, W.
R., Feringa, B. L., Hoogenboom, J. P.,
Hosson, J. T. M. D., & Dorp, W. F. V. (2012).
Selective Functionalization of Tailored
Nanostructures. Acs Nano,
6(10), 9214-9220. https://doi.org/10.1021/nn303571p
Tinnefeld,
P., & Cordes, T. (2012). 'Self-healing'
dyes: intramolecular stabilization of organic fluorophores.
Nature Methods, 9(5), 426-427. https://doi.org/10.1038/nmeth.1977
2011
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. https://doi.org/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. https://doi.org/10.1039/c0cp01919d
2010
Vogelsang,
J., Cordes, T., Forthmann, C., Steinhauer, C., &
Tinnefeld, P. (2010). Intrinsically Resolution Enhancing
Probes for Confocal Microscopy. Nano
Letters, 10(2), 672-679. https://doi.org/10.1021/nl903823s
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. https://doi.org/10.1002/cphc.201000189
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. https://doi.org/10.1021/jp107899g
Cordes,
T., Strackharn, M., Stahl, S. W., Summerer, W., Steinhauer,
C., Forthmann, C., Puchner, E. M., Vogelsang, J., Gaub, H. E.,
& Tinnefeld, P. (2010). Resolving Single-Molecule
Assembled Patterns with Superresolution Blink-Microscopy.
Nano Letters, 10(2), 645-651. https://doi.org/10.1021/nl903730r
Cordes,
T., Santoso, Y., Tomescu, A. I., Gryte, K., Hwang, L. C.,
Camará, B., Wigneshweraraj, S., & Kapanidis, A. N. (2010).
Sensing DNA Opening in Transcription Using Quenchable
Förster Resonance Energy Transfer.
Biochemistry, 49(43), 9171-9180. https://doi.org/10.1021/bi101184g
Cordes,
T., Vogelsang, J., Anaya, M., Spagnuolo, C., Gietl, A.,
Summerer, W., Herrmann, A., Muellen, K., Tinnefeld,
P., & Müllen, K. (2010). Single-Molecule Redox
Blinking of Perylene Diimide Derivatives in Water.
Journal of the American Chemical Society,
132(7), 2404-2409. https://doi.org/10.1021/ja9099714
2009
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. https://doi.org/10.1073/pnas.0811875106
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. https://doi.org/10.1007/s00339-009-5169-3
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. https://doi.org/10.1021/ja809117z
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. https://doi.org/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. https://doi.org/10.1039/b822318c
Böttcher,
C., Zeyat, G., Ahmed, S. A., Irran, E., Cordes, T.,
Elsner, C., Zinth, W., & Rueck-Braun, K. (2009).
Synthesis of novel photochromic pyrans via palladium-mediated
reactions. Beilstein Journal of Organic
Chemistry, 5(25), 1-7. https://doi.org/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. https://doi.org/10.1016/j.jphotochem.2009.05.015
Cordes,
T., Elsner, C., Herzog, T. T., Hoppmann, C., Schadendorf,
T., Summerer, W., Rück-Braun, K., & Zinth, W. (2009).
Ultrafast Hemithioindigo-based peptide-switches.
Chemical Physics, 358(1), 103-110.
https://doi.org/10.1016/j.chemphys.2008.12.027
Cordes,
T., Herzog, T. T., Malkmus, S., Draxler, S., Brust, T.,
DiGirolamo, J. A., Lees, W. J., & Braun, M. (2009).
Wavelength and solvent independent photochemistry: the
electrocyclic ring-closure of indolylfulgides.
Photochemical & Photobiological Sciences,
8(4), 528-534. https://doi.org/10.1039/b817627b
2008
Cordes,
T., Malkmus, S., DiGirolamo, J. A., Lees, W. J., Nenov, A.,
Vivie-Riedle, R. D., Braun, M., & 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. https://doi.org/10.1021/jp807097w
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. https://doi.org/10.1016/j.cplett.2008.02.096
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. https://doi.org/10.1021/jp077472l
2007
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). University of Groningen, The Zernike Institute for
Advanced Materials.
Schrader,
T. E., Schreier, W. J., Cordes, T., Koller, F. O.,
Babitzki, G., Denschlag, R., Renner, C., Löweneck, M., Dong,
S-L., Moroder, L., Tavan, P., & 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. https://doi.org/10.1073/pnas.0707322104
Cordes,
T., Heinz, B., Regner, N., Hoppmann, C., Schrader, T. E.,
Summerer, W., Rück-Braun, K., & Zinth, W. (2007).
Photochemical Z→E Isomerization of a
Hemithioindigo/Hemistilbene ω-Amino Acid.
Chemphyschem, 8(11), 1713-1721. https://doi.org/10.1002/cphc.200700223
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. https://doi.org/10.1016/j.chemphys.2007.06.048
Zinth,
W., Schrader, T. E., Schreier, W. J., Koller, F. O., Cordes,
T., Babitzki, G., Denschlag, R., Tavan, P., Löweneck,
M., Dong, S-L., Moroder, L., & 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). University
of Groningen, The Zernike Institute for Advanced Materials.
2006
Cordes,
T., Weinrich, D., Kempa, S., Riesselmann, K., Herre, S.,
Hoppmann, C., Rück-Braun, K., & Zinth, W. (2006).
Hemithioindigo-based photoswitches as ultrafast light trigger
in chromopeptides. Chemical Physics
Letters, 428(1), 167-173. https://doi.org/10.1016/j.cplett.2006.07.043
2004
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. https://doi.org/10.1016/j.vacuum.2003.12.107
| Last modified: | 20 January 2016 12.41 p.m. |