Proteins perform key biological functions, such as catalyzing chemical reactions or detecting environmental changes. Thomas Perkins investigates the stability of and the mechanical forces generated by protein motors such as helicases that unzip a double-stranded piece of DNA as they move along it. Researchers in his group attach one end of the DNA to a tiny bead, which is held in place by optical tweezers (the equivalent of the optical dipole trap used in atomic physics). The other end of the DNA is bound to a helicase that is attached to the surface of a glass cover slip. When chemical energy (in the form of ATP) is added to the helicase, the enzyme begins to translocate along the DNA. Using precision optical techniques, the Perkins group then measures the change in position of the bead in nanometers and the forces generated by the enzyme in piconewtons. The group hopes the experiments will lead to a model of how the enzyme uses ATP to move along DNA and help characterize the interactions of the protein with the base sequences of the DNA. Thanks to a recently awarded W. M. Keck Grant in RNA sciences, the Perkins group is starting new experiments to investigate the mechanical stability of RNA and RNA-protein complexes.

Optical microscope stabilization

Following in JILA's tradition of precision measurements, the Perkins group is working to improve the resolution of optical tweezers by increasing sensitivity while reducing system noise. Improvements include the use of a more stable optical design (with improved laser-pointing stability and reduced microscope-stage drift), active sample stabilization, and the introduction of a grid of nanofabricated fiducial marks. The fiducial marks eliminate problems with beads not firmly coupled to the cover slip and with random bead distribution on the cover slip. The Perkins group is investigating new materials for optical trapping. Recently, large gold nanoparticles were shown to increase trapping efficiency and detection sensitivity, but they also caused too much heating for temperature-sensitive-optical-trapping experiments.