Visualizing Single DNA-bound proteins using DNA as a scanning probe

A loop in our genetic material

By grabbing the ends of DNA with laser beams, one can make DNA do very unusual things. It is even possible to put a loop in a DNA molecule and slide it along a second DNA molecule, even though DNA and proteins are much too small to see with a microscope! This way, researchers of the Physics of Complex Systems group in the Laser Centre (VU University, Amsterdam) have been able to see that certain proteins bind to specific locations on the DNA.

In the team of Dr. Wuite, biophysicists use so-called "optical tweezers" to grab plastic beads with a diameter of only a thousandth of a millimeter, that are visible under a microscope. The beads are caught in the focal point of a focused laser-beam. If the laser beam moves, the beads move along with it. By sticking the ends of a DNA molecule to beads, the researchers can bend, twist and stretch the DNA anyway they like. Meanwhile, they use the laser light that scatters off the beads to precisely measure the forces exerted on the DNA.

Researchers Maarten Noom, Bram van den Broek and Joost van Mameren, working in the team of Wuite, have demonstrated for the first time that with four optical tweezers it is possible to wind two molecules around each other. Like miniature ropes, they used one of the DNA molecules to make a loop tightly around the other. Next, they pulled this loop carefully along the second DNA molecule. Interestingly, the researchers discovered that the DNA molecules could slide along each other with hardly any friction. However, when they had proteins bound to the DNA, these ‘obstacles’ caused the loop to get stuck briefly. In this way the researchers could detect at which locations specific proteins bind to DNA. Moreover, when the loop is pulled tighter, they can even wipe bound proteins off the DNA.

The new technique was published in the December 2007 issue of the journal Nature Methods. This technology for manipulating two DNA molecules provides a powerful means to study complex biological processes that involve multiple pieces of DNA, such as the compaction of DNA and the DNA replication machinery. With existing techniques these processes are hard to control and investigate. Therefore, the new 'dual DNA' technique represents an important new tool in bio-nanotechnology.