BioWorld International Correspondent

Applied Biosystems Inc. needs 18,000 PCR TaqMan probes to provide 50 percent coverage of the human genome, said Lars Kongsbak, CEO of privately held Danish company Exiqon A/S.

His firm in March will introduce a new approach to PCR, he said, which will require just 90 probes but will provide 98 percent coverage of the expressed genome or transcriptome.

"It's basically twice as good," he said.

The Vedbaek-based company has developed a set of real-time PCR detection probes based on its locked nucleic acid (LNA) technology, a DNA analogue comprising 2'-O,4'-C-methylene bicyclonucleoside monomers. They obey normal Watson-Crick base-pairing rules but have enhanced binding affinities for complementary DNA or RNA sequences.

That property, said Kongsbak, has enabled the company to develop PCR probes for quantitative analysis of gene expression that contain just nine bases, whereas conventional probes typically contain about 20. That, in turn, has allowed it to gain coverage with a small library of probes, since the human transcriptome, Kongsbak said, is heavily biased toward certain 9mer sequences. The sequences contained in the 90 probes Exiqon has developed collectively occur 650,000 times throughout the genome.

"This has not been published yet," he said. "I don't think this is generally known, and the application of this knowledge is patent protected by Exiqon." Despite the redundancy of the amplification detection probes, users of the system will still be able to fish out an individual gene of interest, as the primers used in a particular reaction will be unique to that gene.

Exiqon plans to sell its collection of probes along with access to a web portal that will provide information on assay conditions, appropriate primer sequences and the correct probe to use.

"You save time because now you don't have to order a new probe every time you have a new gene of interest," Kongsbak said. The system is in use at a small number of beta sites in Europe. "So far it's very robust," he said.

LNA was discovered by Jesper Wengel, of Copenhagen University in Denmark, and by Takeshi Imanishi at Osaka University in Japan. Exiqon, which was founded in 1996, owns the technology but licensed therapeutic applications to another Danish firm, Cureon, now part of Santaris Pharma A/S, of H rsholm.

Exiqon closed the year by raising $3 million from existing investors Scandinavian Life Science Venture, TeknoInvest, Nobel Group and LD. The company has raised nearly $25 million to date and has logged cumulative revenues of around $12 million. It now has 21 employees, following two major rounds of job cuts and the adoption of a new strategy.

"Part of the turnaround has been to open the box, so to speak, and let other companies gain access to our technologies," Kongsbak said. During the past year, the company has signed around 15 licensing agreements for LNA and for a second technology, AQ-Link, a method for light-dependent attachment of macromolecules to solid supports.