Isis Pharmaceuticals (NASDAQ:ISIS) jumped almost 10% yesterday on news of positive Phase II trial results from its rheumatoid arthritis (RA) drug candidate, ISIS 104838 (alas, no cool trade name yet). About 40% of patients achieved a significant improvement in their disease, compared to about 20% of the placebo group.

While Amgen's (NASDAQ:AMGN) blockbuster RA drug, Enbrel, still appears to be the most powerful drug on the market, there are several potential advantages to Isis' candidate, which acts on the same inflammatory agent in the body.

The first is cost: Enbrel costs about $14,000 per patient, per year. If 104838 is approved, it will likely cost significantly less. Furthermore, Enbrel needs to be injected twice per week, while in this trial, Isis' candidate appeared just as effective in either once-per-week, or twice-per-week dosings. Finally, and most significantly, Isis' candidate could eventually be available in pill form, whereas Enbrel will always be an injectable drug.

All of this is well and good, and news like this is sufficient to move any biotech 10% on any given day. However, I believe this news is more significant for Isis, as it represents a major success for their "second-generation" anti-sense drugs.

Isis is an old codger of a biotech company, founded back in 1989. The researchers who founded it had a vision of using short strands of DNA or RNA to block production of disease-causing proteins inside cells. It has always been an elegant vision, yet one fraught with major pitfalls. The two main problems are keeping these strands of DNA or RNA stable in the blood, and then actually getting it into the body's cells. These issues have long made me quite bearish on anti-sense technology, especially the first generation of drug candidates.

The only approved drug that Isis has developed in 15 years is Vitravene, which is a special case, as it is directly injected into the eye and doesn't have to travel through the blood or go through many cells. There have been several high-profile failures such as Affinitak. The cancer drug's failure seemed to affirm that anti-sense strategy may be "anti-sense" to investors making a profit.

However, given the recent trial results, I think anti-sense might finally start making better sense -- as well as more cents -- for Isis.

David Nierengarten, Ph.D., works with a biotechnology venture capital fund. He often contributes to Fool.com and is an active member of the TMF community as DavidMN. He does not own shares of any of the companies mentioned. He appreciates your comments at davidnierengarten@mac.com and on the Biotechnology discussion board.