Links und Funktionen




The Cordes group specializes in the development and application of novel spectroscopy and imaging techniques that allow to map structure and function of biomolecules and (bio)chemical processes in space and time. For this the group uses a combination of optical techniques (single-molecule fluorescence spectroscopy & super-resolution imaging) with nanoscale sensors, i.e., fluorescent probes. The Cordes group follows a question-driven approach to gain insight into the molecular mechanisms of membrane transport and is active in developing fluorescent probes and biophysical assays to characterize (bio)chemical processes and structures in vitro and in vivo.


Research Area 1 (Physical Biology): Molecular mechanisms of membrane transport

Membrane transport proteins play crucial roles in numerous cellular processes. Despite their importance, all proposed molecular models for transport are based on indirect evidence due to the inability of classical biophysical and biochemical techniques to directly visualize structural dynamics. This lack of data to validate mechanistic models for transport concerns both primary and secondary active transporters. The Cordes group is using single-molecule tools to decipher the molecular mechanisms of transport of these complex machines directly. This novel biophysical research area will support the development of new strategies against pathogenic bacteria or multi-drug resistant cancer cells.


1) A. Aminian Jazi, et al. „ Single-molecule Förster-resonance energy transfer using temporal separation of fluorescent signals by caged fluorophores “, Biochemistry 56 (2017) 2031-2041.

2) G. Gouridis, et al. „Conformational Dynamics in Substrate-Binding Domains Influence Transport in the ABC Importer GlnPQ“, Nature Structural and Molecular Biology 22 (2015) 57-64.

3) F. Husada, et al. „Watching conformational dynamics of ABC transporters with single-molecule tools “, Biochemical Society Transactions 43 (2015) 1041-1047.


Research Area 2 (Synthetic Biology): Probe development, spectroscopy & biolabelling

Fluorescence emission has evolved to an indispensable tool in the life sciences, e.g., as a general contrast mechanism for imaging, biochemical assays, medical screening, or DNA-sequencing. The merits of these applications and their information content are not limited by physical instruments, but by the performance of the employed fluorescent reporters. These intrinsically suffer from transient excursions to dark states limiting signal height and stability as well as from irreversible photochemical destruction (“photobleaching”) that restricts their observation time. The Cordes lab is developing novel fluorophores with self-healing or other functional properties imparted by the covalent linkage of e.g., photostabilizers to the fluorophore – see a video here. These vastly improved properties have proven to be crucial for advanced fluorescence applications and super-resolution microscopy (STED & STORM). Current projects focus on optimization of chemical linkage of photostabilizer-dye conjugates and their application in live-cells.


1) J. H. M. van der Velde, et al. „A Simple and Versatile Design Concept for Fluorophore Derivatives with Intramolecular Photostabilization“, Nature Communications 7:10444 (2016).

2) N. C. Robb, et al. „Single-molecule FRET reveals the influenza A virus promoter RNA in pre-initiation and initiation conformations“, Nucleic Acids Research 44 (2016) 10304-10315.

3) P. Tinnefeld & T. Cordes: „’Self-Healing Dyes’ – Intramolecular Stabilization of Organic Fluorophores“, Nature Methods 9 (2012) 426-427.


Research Area 3 (Physical Biology): Novel biophysical assays

The Cordes group is using their photophysical expertise to develop novel biophysical tools to answer mechanistic questions in molecular biology. In typical single-molecule assays used for structural mapping of protein complexes, only a single distance is determined per experiment. One of the recent developments used a combination of photophysical (or photochemical) properties to obtain a multi-dimensional assay with higher information content: While a fluorescence resonance energy transfer process (FRET) reports on the distance (changes) between the two fluorophores the novel assay simultaneously allows to detect the presence of and distance to another yet unlabelled biomolecule via protein-induced fluorescence enhancement.


1) A. Aminian Jazi, et al. „ Single-molecule Förster-resonance energy transfer using temporal separation of fluorescent signals by caged fluorophores “, Biochemistry 56 (2017) 2031-2041.

2) E. Ploetz, E. Lerner, et al. „PIFE and FRET as synergetic multi-scale molecular rulers“, Scientific Reports 6:33257 (2016).

3) E. Lerner, E. Ploetz, et al. „A quantitative theoretical framework for PIFE-FRET“, Journal of Physical Chemistry B 120 (2016) 6401-6410.

4) J. Hohlbein, et al. „Alternating Laser Excitation: Single-Molecule FRET and Beyond“, Chemical Society Reviews 43 (2014) 1156-1171.

5) T. Cordes & S. A. Blum: „Opportunities and Challenges in Single-Molecule and -Particle Fluorescence Microscopy for Mechanistic Studies of Chemical Reactions“, Nature Chemistry 5 (2013) 993-998


Research Area 4 (Physical Biology): Time-resolved spectroscopy

The Cordes lab is in the process to setup femtosecond transient absorption spectroscopy in the visible spectral range with the goal to characterize biologically interesting processes. In particular we will study the excited state dynamics of (non-canonical) DNA nucleobases to reveal evolutionary selection criteria, i.e., which photophysical and photochemical pathways were optimized to maintain high stability of DNA especially in the early phases of life. Furthermore we are interested in energy and electron transfer pathways of photosynthetic complexes where parts of the antenna complex are not yet fully assembled or coupled to hybrid structures with inorganic materials.


1) Herzog et al., "The photochemical ring opening reaction of chromene as seen by transient absorption and fluorescence spectroscopy", Photochemical & Photobiological Sciences (2013)

2) Graupner et al., "Photoisomerization of Hemithioindigo compounds: Combining Solvent-and Substituent Effects into an Advanced Reaction Model", Chemical Physics (2018)