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.
Movie of the experiment
In the movie (sped up 3x) one can see how first four beads are caught by (invisible) optical tweezers. Next, two beads start moving ‘searching for DNA. If they ‘catch’ DNA, the stationary bead moves a little bit along with the moving bead as if there were an invisible wire. Because this is hard to see, crosshairs have been added at the moment this effect is visible. After the DNA is caught it is wound around each other by de-focusing one of the beads. The beads have a diameter of 2 micrometer. The DNA is 16.4 micrometers in length (one micrometer is one thousandth of a millimeter).