The dynamics and mechanics of DNA and DNA-binding proteins

The genetic information of an organism is encoded in the base-pair sequence of its DNA. Many specialized proteins are involved in handling DNA and processing the vast amounts of information on the DNA. In order to do this swiftly and correctly, these proteins have to move quickly and accurately along and/or around the DNA. Some examples are: DNA replication during cell division by DNA-polymerase, bacterial defense against invading viral DNA by restriction endonucleases and the search for and repair of UV-induced damage of DNA by uvrABC enzymes. Other proteins such as histones (in eukaryotes) and nucleoidassociated proteins (in bacteria) bind more rigidly to DNA to compact it and to regulate the expression of genes. We use advanced single-molecule techniques such as optical tweezers, scanning-force microscopy and single-molecule fluorescence to study the mechanism of DNA-binding proteins. Currently we investigate the mechanical properties of DNA itself, DNA polymerase, the protein that copies DNA and RNA polymerase, the protein that reads the DNA sequence, while generating RNA. In addition we are interested in DNA repair mechanisms, such as homologous repair and the way DNA is dynamically organized in chromatin by so-called nucleoid-associated proteins (such as HU, H-NS, IHF and Fis) or nucleosomes.

 Wuite_Peterman

Artist's impression of force-induced DNA melting. When DNA is extended using optical tweezers (red cone represents laser focus, white globe microsphere attached to DNA end) and a high tension is applied, it melts: the base pairs connecting the two strand break and the double helical structure vanishes. Two single strands of DNA are left over.

Contact: Gijs Wuite, e-mail: GJL.Wuite@few.vu.nl and Erwin Peterman, e-mail:EJG.Peterman@few.vu.nl