Scientist I​/II, Nucleic Acid Chemistry

The Company

We are Alloy Therapeutics
—a biotechnology ecosystem company empowering the global scientific community to make better medicines together. Through a community of partners, we democratize access to pre-competitive tools, technologies, services, and company creation capabilities that are foundational for discovering and developing therapeutic biologics. The company facilitates affordable, non-exclusive access to the entire drug discovery community from academic scientists, small and medium biotech, to the largest biopharma.

At Alloy, we believe our industry should compete on getting the best drugs to patients as quickly as possible, not exclusive access to the best platforms. As a reflection of our relentless commitment to the scientific community, we reinvest 100% of our revenue in innovation and access to innovation. MAY THE BEST DRUG WIN.

Alloy is headquartered in Waltham, MA with additional labs in Cambridge, UK;
Basel, Switzerland, and Athens, GA. Successful members thrive in our shared culture of accountability, deliberate trust, and open communication. As a team we aspire to work together to exceed expectations and collectively contribute across the global organization to always maintain our nimble, startup culture.

This is an on‑site and full‑time position in Waltham, MA. At Alloy, we have an ethos of “Mentorship‑By‑Apprenticeship” in all of our positions. We strive to have workers in the office when needed to interact organically and face‑to‑face. Of course, as a lab‑based operation, our cells and animals grow 7 days a week, 365 days per year. We respect and value our colleagues for their hard work that requires them to be in the lab every day.

We ask our people who have more flexible accommodations, like this position, to appreciate their colleagues who have less flexibility. We are all one team!

The Alloy Genetic Medicines group is innovating a novel RNA‑based drug discovery platform, namely “Anti Clastic”, spanning the fields of antisense therapeutics to immunomodulating therapeutics. This technology platform was launched by Alloy in 2023 after exclusively licensing its underlying intellectual property which implements a novel spatial conformation of the oligonucleotide developed by Sudhir Agrawal of Arnay Sciences. The team works closely with external partners to discover and develop Anti Clastic RNA medicines.

This position reports to the Head of Nucleic Acid Chemistry. We are seeking a detail‑oriented Nucleic Acid Chemistry Scientist to join our growing Nucleic Acid Chemistry team supporting the CMC development of oligonucleotides, mRNA, pDNA templates, and antibody‑oligonucleotide conjugates (AOCs). The successful candidate will bring strong hands‑on expertise in synthesis and purification of nucleic acids, as well as HPLC and LC‑MS analytics for RNA, DNA, and nucleic acid medicines.

You will have a proven track record of developing, documenting, qualifying, and troubleshooting analytical methods and production processes in a fast‑paced industrial environment. This role also requires experience working with and managing Contract Research Organizations (CROs), and developing/synthesizing reference materials to enable method development and program progression.

This role may be filled at Scientist I or Scientist II depending on experience and demonstrated level of independence.

• pDNA Production:
  Execute microbial fermentation (E. coli) for plasmid DNA amplification; perform harvesting, lysis, and purification of pDNA.
• Linearization:
  Perform enzymatic restriction digests to linearize pDNA templates for downstream transcription.
• mRNA Synthesis:
  Lead in vitro transcription (IVT) reactions to produce mRNA, including enzymatic capping (Cap
  1) and poly‑adenylation.
• Oligonucleotide:
  Execute procedures to synthesize oligonucleotides.
• Purification:
  Utilize TFF (Tangential Flow Filtration) and chromatography (IEX, HIC, or Affinity) to purify intermediates and finished products from process‑related impurities.

• Develop, optimize, document, qualify, and transfer…