When it comes to RNAi therapeutics company Alnylam (NASDAQ: ALNY), Merck's loss (NYSE: MRK) is Sanofi's (NYSE: SNY)'s gain.

Merck is selling RNAi company Sirna -- a 2006 $1.1 billion acquisition bought in the midst of a boom surrounding RNAi technology -- to Alnylam for $175 million with only $25 million in cash. Even with $105 million promised in milestones and some royalties, Merck will not likely recoup its losses as it finalizes the moves it made to back away from RNAi in 2011 with the closure of its San Francisco Sirna research facility.

Simultaneously, while Merck is backing away, Sanofi is adding an additional $700 million  to its stake in Alnylam .

Alnylam is no stranger to fluid Big Pharma partnerships, having struck various deals with Takeda Pharmaceuticals, GlaxoSmithKline, Biogen Idec, Medtronic, Roche, Pfizer, Bristol-Myers Squibb and others.

Those partnerships have always been somewhat unstable. In 2005 it partnered with Novartis on 31 drug targets, making Novartis the second-largest shareholder at the time. The partnership ended in 2010, resulting in large layoffs for Alnylam .

 Similarly, in July 2007, Roche made a $1 billion dollar deal with Alnylam for nonexclusive licensing rights. In 2010, Roche, in the midst of major cuts, terminated its efforts in RNAi , spiraling not only Alnylam but the entire field of RNAi drug development into uncertainty.

So why all the flux?
Alnylam is a pioneering company in RNA interference (RNAi), a relatively novel discovery from 1998 that earned its scientists a Nobel Prize in 2006. Since then, pharmaceutical companies have spent billions trying to harness the discovery into therapeutics.

The technology works at the level of RNA to silence genes from producing the small molecules or proteins that conventional drugs target. As such, cancers, respiratory diseases, metabolic disorders and liver diseases that were previously untouchable by drug therapies could potentially be treated.

The discovery of RNAi set off a race to the first therapy with Alnylam and its many various and changing partnerships just one part of the complex web. As the reality of the timeline to drug development struck, companies started backing away from RNAi as a field, with Roche's 2010 retreat signaling a major chill for the field.

Nonetheless, Alynylam has continued its efforts in R&D and demonstrated methods that addressed the difficulty of delivering an extracellular drug intracellularly to where the gene targets are housed. The company presented data indicating tumor shrinkage in liver cancer from RNAi therapies and also have active trials for therapies for cholesterol, amyloidosis , hemophilia and others. Meanwhile, competitors like Arrowhead Research have been making movement on RNAi candidates for hepatitis B as well as doing their own work on nanoparticles that complement RNAi drug delivery.

Sanofi's increased investment in RNAi may signal the thawing of the field and spur others in Big Pharma to follow. Already Roche has partnered with Alnylam's competition Isis Pharmaceuticals and Santaris, and Monsanto had done the same with Tekmira. As a result, the verdict is out on specifics for Alnylam's portfolio and pipeline, but RNAi as a field is likely on its way to a comeback.

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Fool contributor Amy Ho has no position in any stocks mentioned. The Motley Fool recommends Alnylam Pharmaceuticals and Isis Pharmaceuticals. The Motley Fool owns shares of Medtronic. Try any of our Foolish newsletter services free for 30 days. We Fools may not all hold the same opinions, but we all believe that considering a diverse range of insights makes us better investors. The Motley Fool has a disclosure policy.