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Berkeley scientists get first detailed look at Dicer

Dicer enzyme in Giardia is identical to the core of a Dicer enzyme in higher eukaryotes, including humans, that cleaves dsRNA into lengths of about 25 bases.

In their Science paper, Doudna and her colleagues describe a front view of the structure as looking like an axe. On the handle end there is a domain that is known to bind to small RNA products, and on the blade end there is a domain that is able to cleave RNA. Between the clamp and the cleaver is a flat-surfaced region that carries a positive electrical charge. Doudna and her colleagues propose that this flat region binds to the negatively charged dsRNA like biological Velcro, enabling Dicer to measure out and snip specified lengths of siRNA.

"When you put the clamp, the flat area and the cleaver together, you get a pretty good idea as to how Dicer works," Doudna said. "We're now using this structural model to design experiments that might tell us what triggers Dicer into action."

Different forms of the Dicer enzyme are known to produce different lengths of siRNA. Having identified the flat-surfaced positively charged region in Dicer as the "ruler" portion of the enzyme, it may be possible to alter the length of a long connector helix within this domain to change the lengths of the resulting siRNA products.

"One size does not fit all for Dicer, it makes dsRNA products that range from 21 to 30 base pairs in length or longer. We would like to see what happens when you take a natural Dicer and change the length of its helix," Doudna said.

Determining Dicer's crystal structure was made possible through the unique crystallography capabilities of ALS Beamline 8.2.1 and 8.2.2, Doudna said. Funded through HHMI, beamlines 8.2.1 and 8.2.2 are powered by a superconducting bend magnet, an ideal source of x-rays for protein crystallography experiments. The "superbend" magnet is used to extract x-rays from a relativistic beam of electrons circulating through the ALS stora
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Contact: Lynn Yarris
lcyarris@lbl.gov
510-486-5375
DOE/Lawrence Berkeley National Laboratory
12-Jan-2006


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