Abstract

Advances in optical imaging and molecular manipulation techniques have made it possible to observe individual molecules and record ‘molecular movies’ that provide new insight into their dynamics and reaction mechanisms. Our group, the Single-Molecule Biophysics group, is a new group at Groningen University and focuses on the development and use of single-molecule tools to understand how proteins work. One of our goals is to study the interactions between proteins and DNA and how these interactions underlie a variety of important biological processes, such as DNA replication and gene expression.

I will discuss recent experiments in which we visualize how proteins that recognize specific, unique sequences on DNA find such targets amidst billions of basepairs of nonspecific DNA . By combining one-dimensional diffusion along the DNA with three-dimensional diffusion through the surrounding solution, these proteins are able to speed up the rate at which they find their targets by many orders of magnitude compared to a scenario in which they would use only three-dimensional diffusion. I will present a simple physical model that describes our data and reconciles the results of many different studies of genomic target search.

Another interest of our group is the application of single-molecule tools to the study of large, multi-protein complexes. I will discuss results of single-molecule studies on the replisome, the protein machinery that is responsible for the faithful duplication of DNA during cell division. By combining the mechanical stretching of single DNA molecules with the single-molecule fluorescence observation of individual components of this machinery, we gain access to a deeper molecular understanding of this biologically important process.