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Senior Scientist, Nucleic Acid Chemistry

Flagship Pioneering
Flagship Pioneering Salary
Cambridge, MA Full Time
POSTED ON 3/23/2026
AVAILABLE BEFORE 7/20/2026
The Company

FL99 is developing novel delivery technologies that will fundamentally redefine how genetic medicines can treat disease. We’re looking for future colleagues who are driven to solve incredibly hard problems in a collaborative, fast-paced environment. If that sounds like you, we’d love to consider your application.

We are seeking an outstanding Senior Scientist, Nucleic Acid Chemistry (exact title flexible based on qualifications) to join us in ideating and building the next generation of Programmable Medicines. Our mission is to completely re-imagine nucleic acid therapeutics, casting aside long-standing dogma to pioneer integrated innovation at the cutting edge of both payload and delivery. This is a rare and unique opportunity to be one of the first employees of a biotech startup that combines an insurgent, swing-for-the-fences mindset with the backing, resources, and know-how of one of biotech’s leading VCs.

Qualifications

  • PhD in Chemistry or Biochemistry with deep experience in nucleic acid chemistry (e.g., synthesizing and applying chemical probes of DNA, developing small molecules to profile RNA structure, or creating tools to study nucleic acid modifications)
  • Expertise in methods for analyzing and purifying compounds (NMR, HPLC, LC-MS, etc.)
  • Fluency in standard molecular biology methods for producing and assaying nucleic acids (PCR, IVT, gel and capillary electrophoresis, etc.)
  • Experience with organic synthesis of small molecules
  • Caring deeply about your work and your colleagues
  • Passion for challenging, fast-paced, ever-changing science
  • Superior attention to detail and execution of experiments, both personally and via CROs

Key responsibilities

  • Contribute to Nucleic Acid Chemistry innovation, aligned with the company’s core strategic ­goals. This role is the first dedicated hire in our Chemistry team, so we’re not just looking for a pair of hands. We’re looking for someone who can think critically and creatively about nucleic acids to influence the company’s scientific directions, including:
    • Molecular design
    • Synthesis scheme optimization
    • Assay design
  • Plan and execute Nucleic Acid Chemistry experiments. Along with ideation, we’re looking for someone who’s excited to roll up their sleeves and pursue benchwork science. This is primarily a bench role, at least at the outset. Key skillsets include:
    • Preparation, purification, and validation of small molecules (NMR, LC/MS, HPLC, etc.)
    • Reactions of small molecules with nucleic acids, including purification and validation
    • CRO management for small molecule synthesis


Who you are



  • Technical expert: Your background is in Chemistry or Biochemistry, and you have relevant experience in nucleic acid innovation, production, purification, and assay development.
  • Mission-driven scientist: You have an unquenchable spirit to build something new that will create huge impact for the world.
  • Relentless pioneer: You thrive in new and unknown territory - capable of charting comprehensive but actionable plans, executing rapidly and iteratively to make progress, and reliably delivering decisive readouts on time.
  • Team player: You flourish in collaborative work environments with other highly skilled individuals. You readily support your colleagues’ challenges & celebrate their victories.
  • Effective communicator: You not only understand the science but are capable of conveying technical information in a clear, concise, and decisive manner.

At Flagship, we recognize there is no perfect candidate. If you have some of the experience listed above but not all, please apply anyway. Experience comes in many forms, skills are transferable, and passion goes a long way. We are dedicated to building diverse and inclusive teams and look forward to learning more about your unique background.

Recruitment & Staffing Agencies:Flagship Pioneering and its affiliated Flagship Lab companies (collectively, “FSP”) do not accept unsolicited resumes from any source other than candidates. The submission of unsolicited resumes by recruitment or staffing agencies to FSP or its employees is strictly prohibited unless contacted directly by Flagship Pioneering’s internal Talent Acquisition team. Any resume submitted by an agency in the absence of a signed agreement will automatically become the property of FSP, and FSP will not owe any referral or other fees with respect thereto

The salary range for this role is $126,000 - $181,500. Compensation for the role will depend on a number of factors, including a candidate’s qualifications, skills, competencies, and experience. FL99 currently offers healthcare coverage, annual incentive program, retirement benefits and a broad range of other benefits. Compensation and benefits information is based on FL99's good faith estimate as of the date of publication and may be modified in the future.

Salary : $126,000 - $181,500

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