Overview

Molecular Biophysics Group

The research themes of the group are currently focused on unraveling the mechanics and dynamics of biological systems using an array of experimental techniques such as AFM, optical tweezers and (single-molecule) fluorescence. By investigating increasingly complex biological processes, we aim to link single molecule research with experimental systems biology. Most of our biophysical questions are solved in collaboration with biochemists, biologists, theoretical physicists and physicians.  

The bacterial nucleoid - The genome of a bacterium is organized by multitudes of proteins in a structure called the nucleoid. Bacteria respond to environmental changes by constantly regulating the transcription activity of their genes within the nucleoid. This dynamic organization of the nucleoid is not well understood. We are currently performing experiment to elucidate the functioning of the nucleoid at various levels, starting from single proteins interacting specifically with DNA, to molecular machinery involved in transcription and regulation, all the way up to emerging properties due to arrays of (non-)specific proteins interacting with each other and with multiple DNA strands.  

 

Viruses are the simplest, smallest and often most rugged forms of life. The protective nanometer-scale proteinaceous shells (capsids) of viruses are particularly striking examples of biological materials evolution. These highly regular, self-assembled, nanometer sized containers are minimalistic in design, but combine complex passive and active functions. Besides chemical and physical protection, they are involved in the selective packing and injection of the viral genetic material. These objects illustrate an interesting array of basic physical principles which we wish to experimentally explore. Using atomic force microscopy, optical tweezers and fluorescence techniques we are studying the physical properties of viral capsids. Moreover, we investigate the mechanism of genome delivery and DNA packaging with single molecule methods.

Homologous recombination - Homologous recombination is essential for maintaining genome integrity. Rad51 is the central eukaryotic recombinase. Strand exchange by Rad51 initiates through the assembly of an ATP-bound nucleoprotein filament on single-stranded DNA. This filament promotes recognition of homologous sequences in a duplex DNA molecule and catalyzes strand exchange between the invading single-stranded DNA and the recipient homologous duplex DNA. The strand exchange reaction results in the formation of a joint molecule that is processed by other enzymes to produce recombinant products. The molecular mechanism by which the recombinase nucleoprotein filament identifies homology and catalyzes strand exchange is a central unsolved puzzle of homologous recombination. This process necessarily involves dynamic rearrangements of protein and dramatic rearrangements of DNA molecules within the nucleoprotein filament.  To study these mechanistic aspects of homologous recombination we have taken a single-molecule approach in which we combine (single) molecule fluorescence with optical manipulation of DNA molecules and proteins.

Artist impression Rad51 disassembling from dsDNA based van Mameren et al. Nature 2009. Image by Tremani.