ed laser beam to trap DNA and other molecules. In a conventional force clamp experiment, microscopic beads are attached near the opposite ends of a long DNA molecule--an arrangement that resembles a weight lifter's dumbbell. A single RNAP enzyme attached to the surface of one bead then moves along the DNA and churns out a complementary strand of RNA, drawing the ends of the dumbbell closer together as it advances. The two beads that form the dumbbell are usually held near the center two separate optical traps. But graduate student William Greenleaf discovered that if one of the two beads in the dumbbell was placed near the outer edge of its trap, the force on it would remain constant, allowing angstrom-level measurements to be made quickly and efficiently.

"That's just what you want--a clamp that allows RNAP to move with impunity, but the force itself doesn't change," Block says. "Normally the bead is inside the trap in the center, but right at the edge of the trap we have this magical property where the force is constant."

Unlike conventional instruments, the new force clamp requires no time-consuming computer computations to correct for competing forces. "This new technique is entirely passive, like a thermos that just sits there and keeps something cool," Block says. "All we have to do is shine light on the system and everything takes care of itself. As a result, we were finally able to resolve the minuscule, 3.4-angstrom steps taken by E. coli RNAP as it transcribes a bacterial gene."

Settling the debates

With these innovations in place, the research team appears to have settled some of the fundamental arguments over DNA-RNA transcription. "Quite simply, our experiment rules out both discontinuous-location models," Block says. "Neither the inchworm nor the scrunching model is consistent with our data, and the idea that some have held all along--that RNAP climbs the DNA ladder one base pair at a time--is probably the righ
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Contact: Mark Shwartz
mshwartz@stanford.edu
650-723-9296
Stanford University
13-Nov-2005

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