Principal Research Associate - Oligonucleotide Chemistry

Role

Location:

Waltham, MA

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. Alloy has evolved from a startup into a global biotechnology infrastructure company operating eleven divisions across five research sites in four countries on three continents.

We are seeking a highly motivated Principal Research Associate to play a key role in augmenting our oligonucleotide chemistry capabilities. This individual will independently drive synthesis, purification, formulation, and analytical characterization of modified oligonucleotides to support discovery and early development programs.

• Independently execute high‑throughput synthesis of modified oligonucleotides using automated platforms (e.g., Mermade, Dr. Oligo, AKTA Oligopilot).
• Optimize and troubleshoot methods for deprotection, purification (reverse‑phase, ion‑exchange), and formulation.
• Operate, maintain, and troubleshoot analytical instrumentation including HPLC, LC‑MS, and UV‑Vis.
• Design and refine analytical methods to assess identity, purity, concentration, stability, and other critical quality attributes.
• Analyze and interpret data to improve yield, purity, and process efficiency.
• Prepare and quantify oligonucleotide materials for in‑vitro and in‑vivo studies.
• Contribute to the development of scalable, reproducible synthesis and purification workflows.
• Establish practical quality control practices appropriate for a growing R&D organization.
• Maintain and troubleshoot essential lab equipment; coordinate servicing and repairs as needed.
• Manage inventory of oligonucleotide sequences, reagents, and critical supplies.
• Maintain clear, accurate, and timely experimental documentation.
• Collaborate closely with cross‑functional teammates in biology, DMPK, and translational sciences to advance program goals.

• BS in Chemistry or related discipline with 5+ years of relevant experience, or MS in Chemistry or related discipline with 2+ years of relevant industry experience.
• Hands‑on experience in oligonucleotide synthesis and purification.
• Demonstrated proficiency with automated oligonucleotide synthesizers.
• Strong experience with HPLC, LC‑MS, and UV‑Vis.
• Experience preparing dosing solutions for in‑vitro and/or in‑vivo studies is a plus.
• Familiarity with laboratory automation (e.g., liquid handlers) is desirable.
• Strong troubleshooting and process optimization skills.
• Ability to work independently with some oversight.
• Excellent organizational skills and attention to detail.
• Strong communication skills and ability to work effectively in a collaborative, fast‑moving team environment.

• You enjoy building systems, not just operating them.
• You take ownership of outcomes, not just tasks.
• You are comfortable working with evolving priorities.
• You proactively identify problems and propose solutions.
• You maintain high standards of scientific rigor, integrity, and lab safety.

• Competitive base and equity compensation commensurate with level of experience and independence.
• 401(k) company match.

• Generous personal and family medical, dental and vision benefits with 100% of premiums and deductibles covered.
• Company‑paid disability (STD, LTD) and life insurance.
• Paid parental leave.
• Family planning support up to $45,000 (e.g., IVF/PGT, adoption, surrogacy, egg retrieval).

• Unlimited PTO and flexible schedules.
• Annual stipend for continuing education with commitment to your career through an individualized professional development plan.
• Wellness and extensive Employee Assistance Program (EAP) including resources for mental wellness.

For this role, the estimated annual base salary range is $80,000 – $95,000, with the final offer based on factors like your experience, skills, and alignment with our needs. Additionally, this role is eligible for equity compensation.

Alloy Therapeutics is an equal opportunity employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, national origin, sex, sexual orientation, gender identity, veteran status, disability, or other legally protected status. If you are unable to submit an application because of incompatible assistive technology or a disability, please contact us at  We will make every effort to respond to your request for disability assistance as soon as possible.