Enzyme measures RNA using natural ruler

For almost a decade, researchers have taken advantage of a powerful process called RNA interference (RNAi) to turn off certain genes in lab organisms and cell cultures (SN: 7/2/05, p. 7: Available to subscribers at Sound Off). Cells also use RNAi as a natural tool in immunity, development, and gene rearrangements within chromosomes. The process begins when a cell chews double-stranded RNA into bite-size fragments of about 25 base pairs, the chemical building blocks of RNA.

Scientists knew that an enzyme called dicer carries out this chopping task, but they hadn’t figured out how dicer measures lengths of RNA so precisely. A new study of dicer’s chemical structure suggests that the enzyme carries a built-in ruler.

Jennifer Doudna of the University of California, Berkeley and her colleagues bombarded dicer with X rays to decipher its structure.

“It was almost immediately clear how the enzyme probably works,” says Doudna.

Team members noticed that dicer is shaped much like a hatchet. A broad area at one end of the molecule contains bladelike protein components that cleave RNA. Extending from these components is a handlelike part that attaches to an RNA strand. The distance from the tip of this handle to the edge of the blade is about the length of 25 base pairs, the team reports in the Jan. 13 Science.

Doudna adds that understanding how dicer works may give researchers clues to how RNAi evolved.