Researchers Create Nanoscale Biomolecule Measurement Tool

Until now, researchers in molecular biology were forced to study changes in DNA by stopping and studying each step one at a time, with little hope of fully capturing the subtleties of molecular changes. That will soon change with the new force-flourescense device developed by a team at the University of Illinois led by physics professor Taekjip Ha.

The device was demonstrated to track the various changes that occur in DNA at the Holliday junction, showing the changes in the 3-dimensional shapes of protein molecules interacting with the helix.

The new technology will permit researchers to study biomolecules as never done before, with structural changes being able to be studied real-time at the nanoscale. The technique involves combining an optical trap, with single-molecule fluorescence techniques, and applies force at the half-pico-newton scale to measure the changes.

The team creatively used lasers and molecular dyes to create the technique. They attached a single molecule of green dye at one point on the protein and a red molecule at another location. They then excited the green molecule with a laser and measured the distance between the pair by the energy transfer. Next, they applied a focused laser to the ends of the molecule, which the notice describes as "functions somewhat like the fictional tractor beam in Star Trek" and allowed the researchers to precisely pull and twist the molecule.

By pairing the two methods, the size and shape of the molecule can be studied while changes are taking place without altering the functionality of the molecule, instead of the more traditional method of freezing the action one step at a time and using destructive electron microscopy. Before, researchers could just hope that the mechanical method would capture the subtleties of the various changes.

The team successfully measured the changes occurring in a Holliday junction, the transitional state where two helixes of DNA slide along each other, compare sequences and repair damage or exchange genes, then unlink and become separate strands again. Scientists have been trying to study this effectively since 1964 when Robin Holliday first proposed the method used by bacteria, yeast, and other organisms in genetic exchanges.

Co-authors of the work are Sungchul Hohng now at Seoul University, physics professor Klaus Schulten, graduate studets Ruobo Zhou, Michelle Nahas and Jin Yu, and molecular biology professor David M. J. Lilley at the University of Dundee, UK.

Ha's team's research into the changes that occurred at the Holliday junction was recently published in the journal Science.