Single Molecule Studies of DNA-protein interactions
We use Optical Tweezers to manipulated single DNA molecules. This method can be used to probe various processes in which the DNA plays a role. In particular, we use this approach to study the interaction between the DNA and sequence specific proteins. Such protein will first search for the appropriate sequence on the DNA and once it has found it will initiate a binding process. These processes will influence the DNA that, in turn, will affect the position of the bead in the optical trap. The displacements that need to be observed in order to monitor such process are in the nanometer range and are the limit of the resolution of such a setup. On the other hand, one could amplify the effect by using a DNA that has several copies of the binding sequence.
Figure: Optical Tweezers trap microbeads that can be attached to single DNA molecules. It is like having a handle at the end of the DNA.