Isis Pharmaceuticals (NASDAQ:ISIS) has long been the champion of antisense technology. It's an elegant idea: influencing messenger RNA (mRNA), a string of nucleotides whose specific sequence provides cells with instructions on which proteins to produce. Antisense drugs are like one side of a zipper whose nucleotide "teeth" link up with complementary "teeth" on an mRNA string, thereby preventing mRNA from delivering its message and blocking the production of proteins implicated in a certain diseases.

Antisense has attracted considerable attention, most recently thanks to Pfizer's (NYSE:PFE) drug-discovery agreement with Isis to identify antisense drugs targeted in ophthalmic disease. Pfizer's not the first company to knock on Isis's door: Other collaborators include Eli Lilly (NYSE:LLY), GlaxoSmithKline (NYSE:GSK), Novartis (NYSE:NVS), Amgen (NASDAQ:AMGN), and Chiron (NASDAQ:CHIR), among others.

Unfortunately, antisense hasn't exactly been a smash success. Isis' many alliances lend credibility to the company's technology, but one shouldn't overestimate the significance of such deals. Pfizer's latest agreement, for example, is modest -- the drug giant will pay Isis $1 million for access to technology and royalties on any drugs resulting from the collaboration. As for Isis' own efforts, since its founding in 1989, the company's only commercial product is Vitravene, a drug launched in 1998 for an eye condition affecting people with AIDS. Even with Vitravene, Isis continues to land in the red; its first-quarter loss from operations amounted to $23.5 million.

In Isis' defense, it has a fairly deep pipeline. The company is preparing for a phase 3 trial for alicaforsen, a compound for ulcerative colitis, and plans to start a phase 2 study for a cholesterol-controlling drug. Still, Isis has seen grand plans fizzle before. Antisense remains an intriguing concept, but investors should keep their fingers crossed.

Fool contributor Brian Gorman is a freelance writer in Chicago. He does not own shares of any companies mentioned in this article.