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1

The Transcription Bubble of the RNA Polymerase–Promoter Open Complex Exhibits Conformational Heterogeneity and Millisecond-Scale Dynamics: Implications for Transcription Start-Site Selection

Robb, Nicole C., Cordes, Thorben, Hwang, Ling Chin, Gryte, Kristofer, Duchi, Diego, Craggs, Timothy D., Santoso, Yusdi, Weiss, Shimon, Ebright, Richard H., Kapanidis, Achillefs N.

Journal:

Journal of Molecular Biology

Year:

2013

Language:

english

File:

PDF, 1.03 MB

english, 2013

2

The complex photo-rearrangement of a heterocyclic N-oxide: Kinetics from picoseconds to minutes

Thorben Cordes, Nadja Regner, Björn Heinz, Elina Borysova, Gerald Ryseck, Peter Gilch

Journal:

Journal of Photochemistry and Photobiology A: Chemistry

Year:

2009

Language:

english

File:

PDF, 1.08 MB

english, 2009

3

Accelerated and Efficient Photochemistry from Higher Excited Electronic States in Fulgide Molecules

Cordes, Thorben, Malkmus, Stephan, DiGirolamo, Jessica A., Lees, Watson J., Nenov, Artur, Vivie-Riedle, Regina de, Braun, Markus, Zinth, Wolfgang

Journal:

Journal of Physical Chemistry A

Year:

2008

Language:

english

File:

PDF, 1.24 MB

english, 2008

4

The Power of Two: Covalent Coupling of Photostabilizers for Fluorescence Applications

van der Velde, Jasper H. M., Oelerich, Jens, Huang, Jingyi, Smit, Jochem H., Hiermaier, Matthias, Ploetz, Evelyn, Herrmann, Andreas, Roelfes, Gerard, Cordes, Thorben

Journal:

The Journal of Physical Chemistry Letters

Year:

2014

Language:

english

File:

PDF, 1.87 MB

english, 2014

5

SPIE Proceedings [SPIE European Conferences on Biomedical Optics - Munich, Germany (Sunday 14 June 2009)] Advanced Microscopy Techniques - Controlling the emission of organic dyes for high sensitivity and super-resolution microscopy

Cordes, Thorben, Stein, Ingo H., Forthmann, Carsten, Steinhauer, Christian, Walz, Monika, Summerer, Wolfram, Person, Britta, Vogelsang, Jan, Tinnefeld, Philip, Campagnola, Paul J., Stelzer, Ernst H. K

Year:

2009

Language:

english

File:

PDF, 441 KB

english, 2009

6

Toward dynamic structural biology: Two decades of single-molecule Förster resonance energy transfer

Lerner, Eitan, Cordes, Thorben, Ingargiola, Antonino, Alhadid, Yazan, Chung, SangYoon, Michalet, Xavier, Weiss, Shimon

Journal:

Year:

2018

Language:

english

File:

PDF, 2.38 MB

english, 2018

7

Kinetic Modelling of Transport Inhibition by Substrates in ABC Importers

de Boer, Marijn, Cordes, Thorben, Poolman, Bert

Journal:

Journal of Molecular Biology

Year:

2020

File:

PDF, 679 KB

2020

8

Photochemical Z→E Isomerization of a Hemithioindigo/Hemistilbene ω-Amino Acid

Thorben Cordes, Björn Heinz , Nadja Regner, Christian Hoppmann, Tobias E. Schrader, Wolfram Summerer, Karola Rück-Braun, Wolfgang Zinth

Journal:

Year:

2007

Language:

english

File:

PDF, 450 KB

english, 2007

9

Make them Blink: Probes for Super-Resolution Microscopy

Jan Vogelsang, Christian Steinhauer, Carsten Forthmann, Ingo H. Stein, Britta Person-Skegro, Thorben Cordes, Philip Tinnefeld

Journal:

Year:

2010

Language:

english

File:

PDF, 1005 KB

english, 2010

10

Ultrafast Hemithioindigo-based peptide-switches

Thorben Cordes, Cord Elsner, Teja T. Herzog, Christian Hoppmann, Torsten Schadendorf, Wolfram Summerer, Karola Rück-Braun, Wolfgang Zinth

Journal:

Chemical Physics

Year:

2009

Language:

english

File:

PDF, 2.44 MB

english, 2009

11

Chemical control of Hemithioindigo-photoisomerization – Substituent-effects on different molecular parts

Thorben Cordes, Torsten Schadendorf, Karola Rück-Braun, Wolfgang Zinth

Journal:

Chemical Physics Letters

Year:

2008

Language:

english

File:

PDF, 334 KB

english, 2008

12

Micro-structured electrode arrays:: high-frequency discharges at atmospheric pressure—characterization and new applications

Lutz Baars-Hibbe, Christian Schrader, Philipp Sichler, Thorben Cordes, Karl-Heinz Gericke, Stephanus Büttgenbach, Siegfried Draeger

Journal:

Year:

2004

Language:

english

File:

PDF, 253 KB

english, 2004

13

On the Mechanism of Trolox as Antiblinking and Antibleaching Reagent

Cordes, Thorben, Vogelsang, Jan, Tinnefeld, Philip

Journal:

Journal of the American Chemical Society

Year:

2009

Language:

english

File:

PDF, 153 KB

english, 2009

14

Linking Single-Molecule Blinking to Chromophore Structure and Redox Potentials

Ingo H. Stein, Stella Capone, Jochem H. Smit, Fabian Baumann, Dr. Thorben Cordes, Prof. Dr. Philip Tinnefeld

Journal:

Year:

2012

Language:

english

File:

PDF, 636 KB

english, 2012

15

Cover Picture: Linking Single-Molecule Blinking to Chromophore Structure and Redox Potentials (ChemPhysChem 4/2012)

Ingo H. Stein, Stella Capone, Jochem H. Smit, Fabian Baumann, Dr. Thorben Cordes, Prof. Dr. Philip Tinnefeld

Journal:

Year:

2012

Language:

english

File:

PDF, 790 KB

english, 2012

16

Selective Functionalization of Tailored Nanostructures

Slingenbergh, Winand, de Boer, Sanne K., Cordes, Thorben, Browne, Wesley R., Feringa, Ben L., Hoogenboom, Jacob P., De Hosson, Jeff Th. M., van Dorp, Willem F.

Journal:

Year:

2012

Language:

english

File:

PDF, 398 KB

english, 2012

17

Real-Time Initial Transcription by a Multisubunit RNA Polymerase

Gryte, Kristofer, Cordes, Thorben, Tomescu, Alexandra, Hwang, Ling, Kapanidis, Achillefs

Journal:

Biophysical Journal

Year:

2011

Language:

english

File:

PDF, 35 KB

english, 2011

18

The photochemical ring opening reaction of chromene as seen by transient absorption and fluorescence spectroscopy

Herzog, Teja T., Ryseck, Gerald, Ploetz, Evelyn, Cordes, Thorben

Journal:

Photochemical & Photobiological Sciences

Year:

2013

Language:

english

File:

PDF, 1.13 MB

english, 2013

19

Mechanisms and advancement of antifading agents for fluorescence microscopy and single-molecule spectroscopy

Cordes, Thorben, Maiser, Andreas, Steinhauer, Christian, Schermelleh, Lothar, Tinnefeld, Philip

Journal:

Physical Chemistry Chemical Physics

Year:

2011

Language:

english

File:

PDF, 2.70 MB

english, 2011

20

'Self-healing' dyes: intramolecular stabilization of organic fluorophores

Tinnefeld, Philip, Cordes, Thorben

Journal:

Year:

2012

Language:

english

File:

PDF, 171 KB

english, 2012

21

Opportunities and challenges in single-molecule and single-particle fluorescence microscopy for mechanistic studies of chemical reactions

Cordes, Thorben, Blum, Suzanne A.

Journal:

Nature Chemistry

Year:

2013

Language:

english

File:

PDF, 1.07 MB

english, 2013

22

Mechanism of Intramolecular Photostabilization in Self-Healing Cyanine Fluorophores

van der Velde, Jasper H. M., Ploetz, Evelyn, Hiermaier, Matthias, Oelerich, Jens, de Vries, Jan Willem, Roelfes, Gerard, Cordes, Thorben

Journal:

Year:

2013

Language:

english

File:

PDF, 2.53 MB

english, 2013

23

Resolving Single-Molecule Assembled Patterns with Superresolution Blink-Microscopy

Cordes, Thorben, Strackharn, Mathias, Stahl, Stefan W., Summerer, Wolfram, Steinhauer, Christian, Forthmann, Carsten, Puchner, Elias M., Vogelsang, Jan, Gaub, Hermann E., Tinnefeld, Philip

Journal:

Year:

2010

Language:

english

File:

PDF, 2.50 MB

english, 2010

24

Sensing DNA Opening in Transcription Using Quenchable Förster Resonance Energy Transfer

Cordes, Thorben, Santoso, Yusdi, Tomescu, Alexandra I., Gryte, Kristofer, Hwang, Ling Chin, Camará, Beatriz, Wigneshweraraj, Sivaramesh, Kapanidis, Achillefs N.

Journal:

Year:

2010

Language:

english

File:

PDF, 3.78 MB

english, 2010

25

Molecular Driving Forces for Z/E Isomerization Mediated by Heteroatoms: The Example Hemithioindigo

Nenov, Artur, Cordes, Thorben, Herzog, Teja T., Zinth, Wolfgang, Vivie-Riedle, Regina de

Journal:

Journal of Physical Chemistry A

Year:

2010

Language:

english

File:

PDF, 4.39 MB

english, 2010

26

The Hammett Relationship and Reactions in the Excited Electronic State: Hemithioindigo Z / E -Photoisomerization

Cordes, Thorben, Schadendorf, Torsten, Priewisch, Beate, Rück-Braun, Karola, Zinth, Wolfgang

Journal:

Journal of Physical Chemistry A

Year:

2008

Language:

english

File:

PDF, 497 KB

english, 2008

27

Folding and Unfolding of Light-Triggered β-Hairpin Model Peptides

Schrader, Tobias E., Cordes, Thorben, Schreier, Wolfgang J., Koller, Florian O., Dong, Shou-Liang, Moroder, Luis, Zinth, Wolfgang

Journal:

Journal of Physical Chemistry B

Year:

2011

Language:

english

File:

PDF, 4.00 MB

english, 2011

28

Intrinsically Resolution Enhancing Probes for Confocal Microscopy

Vogelsang, Jan, Cordes, Thorben, Forthmann, Carsten, Steinhauer, Christian, Tinnefeld, Philip

Journal:

Year:

2010

Language:

english

File:

PDF, 2.69 MB

english, 2010

29

Single-Molecule Redox Blinking of Perylene Diimide Derivatives in Water

Cordes, Thorben, Vogelsang, Jan, Anaya, Milena, Spagnuolo, Carla, Gietl, Andreas, Summerer, Wolfram, Herrmann, Andreas, Müllen, Klaus, Tinnefeld, Philip

Journal:

Journal of the American Chemical Society

Year:

2010

Language:

english

File:

PDF, 3.02 MB

english, 2010

30

Wavelength and solvent independent photochemistry: the electrocyclic ring-closure of indolylfulgides

Cordes, Thorben, Herzog, Teja T., Malkmus, Stephan, Draxler, Simone, Brust, Thomas, DiGirolamo, Jessica A., Lees, Watson J., Braun, Markus

Journal:

Photochemical & Photobiological Sciences

Year:

2009

Language:

english

File:

PDF, 421 KB

english, 2009

31

Single-molecule photophysics of oxazines on DNA and its application in a FRET switch

Vogelsang, Jan, Cordes, Thorben, Tinnefeld, Philip

Journal:

Photochemical & Photobiological Sciences

Year:

2009

Language:

english

File:

PDF, 643 KB

english, 2009

32

Conformational dynamics in substrate-binding domains influences transport in the ABC importer GlnPQ

Gouridis, Giorgos, Schuurman-Wolters, Gea K, Ploetz, Evelyn, Husada, Florence, Vietrov, Ruslan, de Boer, Marijn, Cordes, Thorben, Poolman, Bert

Journal:

Nature Structural and Molecular Biology

Year:

2014

Language:

english

File:

PDF, 1.97 MB

english, 2014

33

[OSA International Conference on Ultrafast Phenomena - Pacific Grove, California (2006..-..)] 15th International Conference on Ultrafast Phenomena - A New Class of Ultrafast Photoswitchable Chromopeptides

Cordes, Thorben, Riesselmann, Kerstin, Herre, Stefan, Rück-Braun, Karola, Zinth, Wolfgang

Year:

2006

Language:

english

File:

PDF, 175 KB

english, 2006

34

Intramolecular photostabilization via triplet-state quenching: design principles to make organic fluorophores “self-healing”

van der Velde, Jasper H. M., Uusitalo, Jaakko J., Ugen, Lourens-Jan, Warszawik, Eliza M., Herrmann, Andreas, Marrink, Siewert J., Cordes, Thorben

Journal:

Faraday Discussions

Year:

2015

Language:

english

File:

PDF, 1.27 MB

english, 2015

35

Superresolution techniques, biophysics with nanostructures, and fluorescence energy transfer: general discussion

Cordes, Thorben, Moerner, William, Orrit, Michel, Needham, Lisa-Maria, Sekatskii, Sergey, Faez, Sanli, Prabal Goswami, Himangshu, Clark, Alex, Meixner, Alfred J., Piatkowski, Lukasz, Sandoghdar, Vahid

Journal:

Faraday Discussions

Year:

2015

Language:

english

File:

PDF, 221 KB

english, 2015

36

Quantum optics, molecular spectroscopy and low-temperature spectroscopy: general discussion

Orrit, Michel, Evans, Geraint, Cordes, Thorben, Kratochvilova, Irena, Moerner, William, Needham, Lisa-Maria, Sekatskii, Sergey, Vainer, Yuri, Faez, Sanli, Vedral, Vlatko, Prabal Goswami, Himangshu, Cl

Journal:

Faraday Discussions

Year:

2015

Language:

english

File:

PDF, 449 KB

english, 2015

37

Plasmonics, Tracking and Manipulating, and Living Cells: general discussion

Cordes, Thorben, Moerner, William, Orrit, Michel, Sekatskii, Sergey, Faez, Sanli, Borri, Paola, Prabal Goswami, Himangshu, Clark, Alex, El-Khoury, Patrick, Mayr, Sandra, Mika, Jacek, Lyu, Guowei, Cros

Journal:

Faraday Discussions

Year:

2015

Language:

english

File:

PDF, 309 KB

english, 2015

38

A Quantitative Theoretical Framework For PIFE-FRET

Lerner, Eitan, Ploetz, Evelyn, Hohlbein, Johannes, Cordes, Thorben, Weiss, Shimon

Journal:

Journal of Physical Chemistry B

Year:

2016

Language:

english

File:

PDF, 985 KB

english, 2016

39

Single-molecule FRET reveals the pre-initiation and initiation conformations of influenza virus promoter RNA

Robb, Nicole C., te Velthuis, Aartjan J. W., Wieneke, Ralph, Tampé, Robert, Cordes, Thorben, Fodor, Ervin, Kapanidis, Achillefs N.

Journal:

Nucleic Acids Research

Year:

2016

Language:

english

File:

PDF, 3.82 MB

english, 2016

40

Förster resonance energy transfer and protein-induced fluorescence enhancement as synergetic multi-scale molecular rulers

Ploetz, Evelyn, Lerner, Eitan, Husada, Florence, Roelfs, Martin, Chung, SangYoon, Hohlbein, Johannes, Weiss, Shimon, Cordes, Thorben

Journal:

Scientific Reports

Year:

2016

Language:

english

File:

PDF, 2.22 MB

english, 2016

41

Synthesis of novel photochromic pyrans via palladium-mediated reactions

Böttcher, Christoph, Zeyat, Gehad, Ahmed, Saleh A, Irran, Elisabeth, Cordes, Thorben, Elsner, Cord, Zinth, Wolfgang, Rueck-Braun, Karola

Journal:

Beilstein Journal of Organic Chemistry

Year:

2009

Language:

english

File:

PDF, 443 KB

english, 2009

42

Caging and Photoactivation in Single-Molecule Förster Resonance Energy Transfer Experiments

Jazi, Atieh Aminian, Ploetz, Evelyn, Arizki, Muhamad, Dhandayuthapani, Balasubramaniam, Waclawska, Izabela, Krämer, Reinhard, Ziegler, Christine, Cordes, Thorben

Journal:

Year:

2017

Language:

english

File:

PDF, 3.82 MB

english, 2017

43

Uptake and Localization of Aminoglycoside Antibiotics in Live Escherichia coli

Warszawik, Eliza M., Smit, Jochem H., Li, Yichen, Loznik, Mark, Paul, Avishek, Cordes, Thorben M., Herrmann, Andreas

Journal:

Biophysical Journal

Year:

2018

Language:

english

File:

PDF, 50 KB

english, 2018

44

How Lipids Modulate Transporter and Channel Function

Ziegler, Christine, Gregor Madej, Matthias, Chandramohan, Arun, Srinivasan Anand, Ganesh, Cordes, Thorben, Aminian, Atieh, Krämer, Reinhard

Journal:

Biophysical Journal

Year:

2018

File:

PDF, 45 KB

2018

45

Photoisomerization of Hemithioindigo compounds: Combining Solvent- and Substituent Effects into an Advanced Reaction Model

Graupner, Franziska.F., Herzog, Teja T., Rott, Florian, Oesterling, Sven, de Vivie-Riedle, Regina, Cordes, Thorben, Zinth, Wolfgang

Journal:

Chemical Physics

Year:

2018

Language:

english

File:

PDF, 2.15 MB

english, 2018

46

How Lipids Modulate Transporter and Channel Function

Ziegler, Christine, Gregor Madej, Matthias, Chandramohan, Arun, Srinivasan Anand, Ganesh, Cordes, Thorben, Aminian, Atieh, Krämer, Reinhard

Journal:

Biophysical Journal

Year:

2018

Language:

english

File:

PDF, 45 KB

english, 2018

47

Conformational dynamics of the ABC transporter McjD seen by single‐molecule FRET

Husada, Florence, Bountra, Kiran, Tassis, Konstantinos, de Boer, Marijn, Romano, Maria, Rebuffat, Sylvie, Beis, Konstantinos, Cordes, Thorben

Journal:

The EMBO Journal

Year:

2018

Language:

english

File:

PDF, 1.09 MB

english, 2018

48

Self-healing dyes for super-resolution fluorescence microscopy

van der Velde, Jasper H M, Smit, Jochem H, Hebisch, Elke, Punter, Michiel, Cordes, Thorben

Journal:

Journal of Physics D Applied Physics

Year:

2019

Language:

english

File:

PDF, 7.06 MB

english, 2019

49

Konformationsbewegungen von aktiven Membrantransportern

Mächtel, Rebecca, Gebhardt, Christian, Cordes, Thorben

Journal:

Year:

2018

Language:

german

File:

PDF, 437 KB

german, 2018

50

On the impact of competing intra- and intermolecular triplet-state quenching on photobleaching and photoswitching kinetics of organic fluorophores

Smit, Jochem H., van der Velde, Jasper H. M., Huang, Jingyi, Trauschke, Vanessa, Henrikus, Sarah S., Chen, Si, Eleftheriadis, Nikolaos, Warszawik, Eliza M., Herrmann, Andreas, Cordes, Thorben

Journal:

Physical Chemistry Chemical Physics

Year:

2019

Language:

english

File:

PDF, 3.78 MB

english, 2019

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