Prof. Don Lamb, Ludwig-Maximilians-University Munich (LMU)

Using Förster Resonance Energy Transfer (FRET), we investigate the dynamics and interactions of individual biomolecules and nanomachines. FRET provides information over distances on the molecular scale (2-10 nm) and can be used to investigate the interaction of single biomolecules as well as the structural changes that occur during their interaction.

As part of this PhD project, the initial steps in the regulation of protein biosynthesis will be investigated. In previous work, we have established that the TATA box Binding Protein (TBP), which recognizes the start position of particular genes on DNA, undergoes a change in behavior when the cofactor NC2 binds to the TBP-DNA complex (Schluesche et al. 2007 NSMB 14, 1196). The observed dynamics opens a new dimension for understanding the control of gene expression. The aims of this project are:

1. To investigate the interaction of TBP with other co-factors.
2. To quantify the effects of alterations in the DNA TATA box sequence.
3. To study the effects of mutations to the TBP and various cofactors and thereby gain mechanistic insights into how genes are regulated.
4. Develop an assay to allow investigations of these interactions under conditions similar to those in the living cell.

As a second aspect of this project, single-molecule FRET methods will be used to investigate protein-nucleic acid interactions. We are currently developing a DNA sensor which allows us to study the conformation of DNA in great detail. Upon binding of proteins to the DNA, the change in DNA conformation can be observed on the single-molecule level. This aims of this project include:

1. Development of three- (and potentially four-) FRET apparatus and analysis methods to investigate the conformation of DNA in the absence and presence of proteins.
2. develop and test different DNA sensors for investigating DNA-protein interactions.
3. Measure the conformational changes of DNA induced by the binding of different DNA-binding changes and the dependence of the sequence on these conformational changes.

Experiment Methods

Fluorescence Spectroscopy  and Microscopy, Single Molecule Methods, two- and three-color FRET, Total-Internal Reflection Fluorescence Microscopy, Protein labeling and purification, Hidden Markov Modeling

Qualifications

A basic understanding of optics and fluorescence spectroscopy is highly desired. Experience with basic computer programming for analysis purposes would be beneficial.

Further information about the research group:
http://www.cup.uni-muenchen.de/pc/lamb/