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New tools speed drug discovery and disease research

To study the genetic components of disease, researchers rely on mice or other research models in which particular genes are silenced, or turned off. In recent years, researchers discovered that they can selectively silence genes using small pieces of RNA called siRNA (short interfering RNA).

Unfortunately, sorting out which siRNA sequences block expression of which genes has proven to be truly daunting. Researchers at Whitehead Institute, however, recently released for public use a new computational tool that will vastly improve this process, streamlining drug discovery and disease research efforts.

A Needle in a Haystack

To harness the power of siRNA, researchers need predictive tools to narrow down the search for siRNA molecules that are most likely to affect a gene in a desired way without affecting the function of other genes. Until now, hunting for siRNA candidates has been like looking for a needle in haystack. Given a gene of 3000 nucleotides, there are 2980 possible siRNA candidates that might affect how the gene functions. (siRNA sequences are approximately 21 nucleotide bases long).

The Biocomputing Group at Whitehead has greatly simplified this process by devising and publishing a web-based tool that can quickly narrow down siRNA candidates.

"Scientists routinely came to Biocomputing asking how they could more efficiently predict siRNA targets," says Lewitter. "Unfortunately, without suitable prediction tools, scientists had to randomly select siRNA strands from a pool of thousands of possibilities and hope that they would be successful in studying a gene of interest."

Faced with scientists' mounting frustration, Biocomputing took on the challenge to develop an easy and efficient tool to predict which siRNA molecules will be effective in a particular experiment. "Using this tool, researchers can narrow down the possibilities of potential siRNAs to a small handful that are likely to be effective for stud
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Contact: Kelli Whitlock
whitlock@wi.mit.edu
617-258-5183
Whitehead Institute for Biomedical Research
12-Mar-2003


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