Associate

Ambion Inc. and German partner Cenix BioScience GmbH, having started their work in earnest just months ago, said they have completed siRNA designs for more than 98 percent of all human, mouse and rat genes listed in the public RefSeq database.

Those small interfering RNAs now are available to researchers. Although the RNA interference field is still burgeoning, there already is a need for better siRNA designs, said Kathy Latham, product manager at Ambion, of Austin, Texas.

"siRNA are short, 21-nucleotide double-stranded pieces of RNA that are complementary to mRNAs of interest," she said. "Up until this point, it has been difficult to discern which bit of the 21 base pairs you need to target. There are some publicly available designs that you could use, but most people find that they don't predict that well."

Latham told BioWorld Today that using the publicly available criteria, only about half of all siRNAs give some sort of knockdown. That percentage drops if seeking a knockdown of more than 70 percent.

"And most want something that destroys more than 70 percent of the messenger RNA in the cell," she said.

The RefSeq database, which stands for Reference Sequence, is a collection of gene sequences from 785,000 proteins and 2,005 organisms freely offered by the National Center for Biotechnology Information. It is the most well known public database, Latham said.

Ambion and Dresden, Germany-based Cenix formed a partnership in December, but "really started this particular project" in March, Latham said. Cenix was founded in 1999 and focuses on genome-based, high-throughput applications of RNA-mediated interference. The companies used a Cenix algorithm capable of accurately predicting siRNA sequences for the work. The algorithm was based on Cenix's experience gained from generating genome-wide RNAi libraries for C. elegans and Drosophila, as well as mammalian cell testing. That experience, Latham said, has translated into "a better algorithm that gives a better proportion of siRNAs that work."

The siRNA designs are available now, and customers can order them through Ambion's website. The price begins at $255 and rises from there, depending on the purification options desired and the synthesis scale.

In May, privately held Ambion raised about $10.5 million. While unable to comment on the company's burn rate or financial position, Latham did say the company was "just fine. We are growing at 30 percent a year and have for the last several years."