By Lisa Seachrist

Washington Editor

Isis Pharmaceuticals Inc. saw its shares jump nearly 16 percent Tuesday after disclosing it had received a U.S. patent for a key enzyme related to antisense technology.

The Carlsbad, Calif.-based company¿s stock (NASDAQ:ISIP) closed at $14.125, up $1.937.

The Patent and Trademark Office granted the company a patent on Human RNase H1, a cellular enzyme that degrades RNA and DNA duplexes. Isis said the patent covers most antisense drugs currently in development as well as the use of antisense technology to identify gene function and validate drug targets.

¿We are very pleased with the issuance of this patent and, frankly, we¿ve earned it,¿ said Stanley Crooke, CEO for Isis. ¿The patent is very broadly enabling and solidifies our dominance in antisense, and we will aggressively pursue the opportunities it presents us.¿

Crooke said almost everyone using an antisense approach to develop drugs will infringe on the newly issued patent. In a conference call he noted that Lexington, Mass.-based Genta Inc.¿s antisense drug G3139, which is being developed as a cancer therapy, almost certainly infringes on Isis¿ patent.

Antisense drugs use DNA oligonucleotides to target specific RNA messengers, the template used to assemble proteins. Once the DNA oligonucleotides bind to the RNA in a cell, RNase H1 destroys the complex preventing the messenger RNA from becoming a protein. ¿In effect, the enzyme kills the messenger,¿ Crooke said.

By inhibiting the production of certain proteins using antisense technology, Isis, as well as other pharmaceutical and biotechnology companies, can explore the function of a gene and validate a gene as a drug target. In January, Isis announced a target validation collaboration with AstraZeneca PLC, of London ¿ the third collaboration of its type.

Sushant Kumar, an analyst with Mehta Partners LLC in New York, noted with this new patent in play, such collaborations may soon become a significant part of the company¿s business.

¿This is a very broad patent,¿ Kumar said. ¿Even if you want to use antisense for target validation, it looks like you¿ll have to talk to Isis. That would encourage companies to collaborate with Isis on target validation. It¿s probably safer that way.¿

The patent covers the DNA sequence for Human RNase H1 as well as vectors and cells containing this DNA sequence and probes to hybridize to the gene or mRNA. The patent includes claims covering methods of making any antisense drug or inhibitor using or relying on the RNase mechanism and specific chemical classes of antisense drugs that work by this mechanism.

¿I don¿t know how they intend to enforce this patent,¿ Kumar said. ¿But, Crooke has said he doesn¿t want to make this technology untouchable.¿

Kumar said the patent could position Isis as an important player in gene expression analysis, noting that if Isis can expand its target validation deals that business could bring in significant revenues.

¿We really think this patent can add meaningful value to the company,¿ Crooke said.