Enabling tool: New microscope allows scientists to track a functioning protein with atomic-level precision

A Stanford University research team has designed the first microscope sensitive enough to track the real-time motion of a single protein down to the level of its individual atoms. Writing in the Nov. 13 online issue of the journal Nature, the Stanford researchers explain how the new instrument allowed them to settle long-standing scientific debates about the way genes are copied from DNA–a biochemical process that’s essential to life. They obtained measurements accurate to one angstrom, or one-tenth of a nanometer. A distance equivalent to the diameter of a single hydrogen atom, and about 10 times finer than any previous such measurement.

Block team focused on a crucial step in the central dogma [central dogma is that in living organisms, genetic information flows from DNA to RNA to proteins], a process known as “transcription,” where each gene is copied from DNA onto RNA. 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.

For the Nature experiment, Block and his colleagues used DNA and RNAP extracted from E. coli bacteria, which is remarkably similar to RNAP in more complex organisms, including humans. “RNAP is one of the most important enzymes in nature,” Block says. “Without it there would be no RNA messages, no proteins and no life.”

In addition to stabilizing the light, the researchers also had to improve the method for detecting force and displacement. Optical force clamps use tiny forces from an infrared 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.

The development of an ultra-stable optical trapping system with angstrom resolution is “a major advance,” says Charles Yanofsky, the Morris Herzstein Professor of Biological Sciences at Stanford and a pioneer of modern molecular genetics. The new device is like “adding movies to stills in understanding enzyme action,” he says.

“This technical achievement will no doubt lead to new information about the molecular machinery that carries out basic cellular processes, particularly those related to replication, transcription and translation,” adds Catherine Lewis, a program director in biophysics at the National Institute of General Medical Sciences (NIGMS).

“If I look in my crystal ball and see where this is going, I think this blows open the field of single-molecule biophysics,” Block says. “We have achieved a resolution for a single molecule comparable to what a crystallographer typically achieves in a millimeter-sized crystal, which has 1,000 trillion molecules in it. Not only are we doing all this with one molecule at one-angstrom resolution, we’re doing it in real time while the molecule is moving at room temperature in an aqueous solution.”