A Stanford University research team with the help of the first microscope sensitive enough to track the real-time movement of a single protein, has settled a long-standing biochemistry dispute. Using the device that allows measurements of 1 angstrom, or 1/10th of a nanometer (a distance equivalent to the diameter of a single hydrogen atom!), the team has proven that RNA polymerase transcribes one DNA base at a time:
Transcription begins when an enzyme called RNA polymerase (RNAP) latches onto the DNA ladder and pulls a small section apart lengthwise. The RNAP enzyme then builds a new, complementary strand of RNA by chemically copying each base in one of the exposed DNA strands. RNAP continues moving down the DNA strand until the gene is fully copied.
“People for years have known that RNA is made one base at a time,” Block says. “But that has left open the question of whether the RNAP enzyme actually climbs up the DNA ladder one rung at a time, or does it move instead in chunks-for example, does it add three bases of RNA, then jump along and add another three bases.” The latter process, called discontinuous elongation, is like reading a book, he explains: “When you read, you don’t advance your eyes one letter at a time. You ‘chunk’: You read it in pieces…”
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 right answer.”
The Stanford group also weighed in on another controversy concerning the actual mechanism that allows RNAP to advance. “RNAP is a molecular motor that starts at one end of the DNA and walks down to the other end,” Block explains. “It gets its energy from the chemical reaction that occurs when it copies A, T, G or C. It’s as if a machine that lays down asphalt could somehow be powered by the asphalt itself.”
Scientists have come up with two different models to explain what drives this molecular motor:
· The power stroke model, in which pent up energy thrusts the enzyme forward-like a loaded spring that’s periodically released.
· The Brownian (or thermal) ratchet model, whereby random thermal energy causes the RNAP enzyme to jiggle back and forth. Each incoming DNA base then locks the enzyme into the forward position so that it cannot jiggle backward. “It would be as if you were repeatedly bouncing off a wall, and every time you happened to bounce a bit farther away, somebody came in and moved the wall up behind you, so you couldn’t bounce so far back. You’d wind up drifting forward, even though your own motion was mostly random,” Block explains.
In the Nature study, Block and his colleagues concluded that the Brownian ratchet model is probably correct for RNAP, even though several other motor proteins are believed to move instead by the power stroke mechanism. “We’ve certainly come down hard in favor of the Brownian ratchet camp and against the power stroke camp,” Block says. “But does that mean all power stroke models have been ruled out and that all Brownian ratchet models are acceptable? No.”
To read more about this fascinating research, go directly to the Stanford press office …