Isis Pharmaceuticals Inc. has earned $3.5 million in milestone payments from Weston, Mass.-based drugmaker Biogen Idec Inc.

Isis received the payment because it began a Phase II clinical trial that was designed to treat infants with spinal muscular atrophy, a rare degenerative genetic disease.

The trial will use drugs derived from Isis’ proprietary “antisense” technology, which engineers RNA molecules to deactivate faulty genes.

Isis has several partnership deals with Biogen Idec, including one made in December that’s worth up to $600 million.

-Meghana Keshavan

— Meghana Keshavan