Carlsbad-based Isis Pharmaceuticals Inc. received $100 million upfront from Weston, Mass.-based pharma giant Biogen Idec Inc. to expand its partnership and develop drugs for neurological disorders.

The deal, which is the fourth between the companies in two years, could be worth up to $320 million. Depending on whether Isis (Nasdaq: ISIS) accomplishes certain developmental goals, it could receive an additional $220 million in milestone payments. The six-year deal gives Biogen Idec exclusive rights to use Isis’ antisense technology to develop therapies for neurological diseases.

Following the announcement, Isis’ stock rose 14 percent, closing day trading Aug. 9 at $31.81 per share — a marked increase for the pharmaceutical company, which was trading at $10.82 at the beginning of the year. Isis now has a market capitalization of $3.67 billion.

Isis’ proprietary antisense technology changes the way genes function, silencing mutations or activating genes to compensate for an underlying genetic defect. The company has developed a massive patent portfolio since it was formed in 1989, and is one of the key stakeholders in the RNA therapies space.

— Meghana Keshavan