The standard tools to probe gene function were either cumbersome, such as knockout mice, or poorly informative, such as gene expression.

RNAi was described in 1998 by Andy Fire and Craig Mello at the Carnegie Institute in Washington, D.C. In plants and lower organisms such as the nematode, RNAi — a process in which double-stranded RNA fragments target and eliminate specific messenger RNA molecules — probably helps defend against viruses and other foreign molecules.

Two years ago, a paper in Nature dramatically showed that RNAi also worked in mammalian cells (Elbashir, S.M. et al. Nature 411, 494-498: 2001). The role of this process in humans remains vague, but, regardless, it possesses immense experimental — and therapeutic — potential.

Fast, easy, and inexpensive — that's what an experimentalist likes to hear. "To my mind, the most important new advance in biology is the RNAi approach," says Tom Cech, president of the Howard Hughes Medical Institute and Nobel laureate for the discovery of RNA enzymes. "RNAi is vastly more powerful than anything we have had. Even people who don't know how to spell RNA can use this successfully in diverse biological systems."

RNAi is already making an impact. Genomewide knockdowns have been carried out in organisms including nematodes. Small interfering RNAs (siRNAs), which silence genes in mammalian cells, are now being designed against as many genes as possible.

One promising approach is to spot cells expressing defined genes on microchips for the analysis (see Ziauddin, J. and Sabatini, D.M. Nature 411, 107-110: 2001). "The hard part is not printing the chips or doing the experiment," says David Sabatini, Whitehead Institute Center for Genome Research Fellow and co-founder of Akceli. "It's picking the right sequences."

Each siRNA contains 21 nucleotides, but some sequences stick better than others. For once, researchers welcome the intense competition. "Hopefully, we will cover different genes, and get to them all more quickly," Sabatini says.

Early adopters of RNAi sound a cautionary note. "We've been using it for about five years," says Geoffrey Duyk, president of R&D at Exelixis. "The dirty little secret of RNAi is that you are knocking down messenger RNA to knock out protein. Because proteins have different turnover rates, you have to have a good way to measure protein level and activity."

Even skittish venture capitalists are falling for RNAi and its potential therapeutic value, with backing for companies such as Cenix and Alnylam Pharmaceuticals.

"The great thing about recombinant DNA and monoclonal antibodies was that they gave actual drugs right from the start," says Christoph Westphal, of Polaris Venture Partners. "With genomics, it just wasn't clear when it would develop a drug."

Firms such as Polaris, which is funding Alnylam, hope RNAi can fuel the next wave of biotech breakthroughs. "If we are very fortunate, siRNAs will make good drugs," Westphal says. "If we are unlucky, we still have a whole natural cellular machinery that is open to small-molecule development."

—Malorye Branca

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