Stellenmarkt / Job Market

Master Thesis:

Opens window for sending emailKatarzyna Krzemien; Opens window for sending emailJens Michaelis


Ph.D. thesis:

Molecular bases of cellular functions

In a cell, myriads of different molecules are corralled together into a crowded environment. Yet, their mutual interactions lead to well-defined cellular structures and enable the cell to perform its vital functions such as gene expression, replication or repair of DNA. The key participating biomolecular species are known for many cellular tasks. To achieve a deeper understanding and thus modeling of cellular processes, we aim to additionally identify the stoichiometry of molecules, the temporal order and dynamics of their interactions and their spatial distribution.
We use and develop modern biophysical and biochemical methods, with a focus on live cell single molecule fluorescence microscopy, to visualize and follow the operation of individual molecules and study their interactions in the natural environment of a living cell.
If you are motivated and interested in working in a young, dynamic and interdisciplinary research group at the exciting limit between Physics and Biology and with cutting-edge technology, please send an email to: Opens window for sending emailChristof Gebhardt


Initiates file downloadWPhD-Stellenausschreibung WS 2013/2014



Ph.D. thesis or Postdoc position:

Molecular mechanism of transcription and transcription coupled repair

The position is part of the new excellence clusters: "Nanoinitiative Munich" and "Munich Cluster for integrated Protein Science", as well as of the Sonderforschungsbereich SFB 646 "Networks in genome expression and maintenance" . The aim of this research is to gain insight into the molecular mechanism of eukaryotic transcription by examining the function of the yeast RNA polymerase II (Pol II) and Rad26, an enzyme involved in transcription coupled repair.
Single-molecule techniques have provided a wealth of information for a huge variety of molecular machines that perform highly specialized tasks inside of the cell. Many of these machines utilize chemical energy to drive a process in a cyclic fashion. Due to the crowded environment inside of the cell and the constant binding and unbinding of proteins, oftentimes these machines must be able to work against an external load, in order to overcome transient barriers. Thus they constitute molecular motors that are driven in a higly efficient manner. Understanding the general principles that underlie the motor function is the common underlying theme behind our research.
We will use single-molecule fluorescence, a novel technique that eliminates averaging over time and/or ensembles of molecules, to study conformational changes and interactions of Pol II elongation bubbles in real-time. While structural studies have given us a great insight into the molecular architecture behind the transciption process, details of the dynamics of this process are currently not well understood. Single-molecule experiments therefore compliment the structural studies by providing real-time, dynamic information.
Furthermore the complex behavior of the elongation process, where phases of rapid transcription are interrupted by distinct pauses, can be investigated directly by single-molecule force spectroscopy. Changes in transcription velocities and effects of transcription factors can be examined with unprecedented detail, allowing for the test of current models of transcription elongation and termination. A better understanding of the molecular details of the transcription process can lead to important insight on how transcription is regulated in vivo.
Transcription coupled repair (TCR), the efficient removal of lesions in the transcribed strand is extremely important for genome maintenance and gene expression. CSB/Rad26, an ATPase related to the Swi/Snf remodeling factors, facilitates TCR. To date, it is not clear, what the precise role of CSB/Rad26 in TCR is. Our aim is to elucidate details of the underlying molecular mechanism by studying the behavior of single Rad26 molecules bound to DNA. A true test for existing models of TCR can be found by investigating the effect of Rad26 on a polymerase that is stalled at a specific DNA lesion.
The experiments will be carried out in close collaboration with the lab of Patrick Cramer (Pol II), the lab of Karl-Peter Hopfner (Rad26) and the group of Thomas Carell (DNA lesions).
We are looking for a skilled and motivated postdoctoral researcher with a background in biochemistry, biophysics or related fields. If you are interested in fast-paced interdisciplinary research at the border of physics, chemistry and biology and would like to work in an international research atmosphere, send your applications including the name and address of two references to:
Opens window for sending emailJens Michaelis


PhD thesis:

Superresolution optical microscopy

For a long time it has been believed that resolution in optical microscopy is limited to about 200nm due to the diffraction of light. For applications of light microscopy in molecular and cellular biology it is, however, extremly important to develop novel methodologies to break this diffraction limit and extend the resolution of optical microscopy down to the level where single proteins can be resolved. The advantage of light microscopy over other existing approaches for applications in biology is that light microscopy allows for the direct investigation of dynamical processes and therefore, besides optical resolution also time resolution is important. A promising technique in this area is the technique of stimulated emission depletion (STED) microscopy. With STED microscopy super-resolution images with video rate time resolution have been demonstrated recently. The aim of the PhD project will be to design and develop a STED microscope for the investigation of higher order chromatin structures. The project is thus at the intersection of physics, chemistry and biology and candidates with a background in biophysics or optical physics are invited to apply for this position.
Interested? Send your applications to: Opens window for sending emailJens Michaelis


PhD thesis:

Nanomechanics of DNA-protein interaction

Enzymes, such as polymerases, helicases or translocases bind to DNA and catalyze biological processes with high specificity and fidelity. We are interested in understanding the underlying molecular mechanisms that drive these marvelous nano-machines. In well defined in-vitro assays we study one molecule at a time with high spatial, and temporal resolution. We use single-molecule fluorescence techniques, to monitor conformational changes as well as movement and rotation. Details about the mechanical properties and mechanisms are elucidated with the help of single-molecule force spectroscopy in optical tweezers, magnetic tweezers or an AFM microscope. We are looking for a skilled and motivated student to combine these two techniques in a new apparatus, to study DNA-protein interaction.
If you are interested in fast-paced interdisciplinary research at the border of physics, chemistry and biology and would like to work in an international research atmosphere, send your applications to: Opens window for sending emailJens Michaelis


Diplomarbeit / Masterthesis:

Experimente mit einzelnen Molekülen an der Grenze zwischen Chemie, Biologie und Physik

Mit diesen und ähnlichen hochaktuellen Fragen beschäftigen wir uns in der Nanomechanics Gruppe von Prof. Jens Michaelis. Wir untersuchen einzelne Biomolekuele, indem wir sie aus Zellen isolieren und dann in einer wohldefinierten Umgebung beobachten. Dabei stützen wir uns auf Methoden der Einzelmolekülfluoreszenz, die es uns ermöglichen Konformationsänderungen der Moleküle oder auch deren Bewegungen direkt zu beobachten. Ausserdem können wir mit ausgeklügelten Lasersystemen auch die Krafte messen, die bei molekularen Prozessen auftreten. Mit diesen neuartigen Methoden ist es nun möglich gängige Modelle für die Funktionsweise der Biomoleküle unter die Lupe zu nehmen und neue Einblicke in molekulare Mechanismen zu gewinnen.
Wir wollen unter anderem untersuchen wie ein einzelnes Gen kopiert wird, wie dabei andere Proteine, die diesen Prozess behindern können, aus dem Weg geräumt werden, und wie gleichzeitig Defektstellen in der DNA repariert werden.
Studenten, die neben dem Interesse für Chemie, sich auch für aktuelle Fragestellungen der Biologie und Physik begeistern, wenden sich bitte an: Opens window for sending emailJens Michaelis