Our lab studies DNA-protein interactions using single molecule micromanipulation techniques. We do experiments on λ-DNA modified with a polystyrene bead on one end and a magnetic bead on the other. By altering the separation between the DNA and a permanent magnet, we can apply various forces to the DNA molecule. You can see some movies of experiments done in our lab using this technique. Image processing methods allow us to extract the extension of the DNA and the force with which it's being pulled. Using microspray protocols and other approaches, we can introduce DNA-binding proteins of interest and observe as they bind to the DNA which is held at a fixed force. When proteins bind and produce changes in the DNA length, say by forming loops in the DNA, the resulting force-extesion curves can be used to infer a great deal of information about the physics of the DNA-protein interaction. Our lab has developed several novel experimental and computational methods to precisely quantify these interactions.
