Principal Research Associate - Oligonucleotide Chemistry

Principal Research Associate – Waltham, MA

As a Principal Research Associate, you will augment the oligonucleotide chemistry capabilities by independently driving synthesis, purification, formulation, and analytical characterization of modified oligonucleotides to support discovery and early development programs.

• Execute high-throughput synthesis of modified oligonucleotides using automated platforms.
• Optimize and troubleshoot deprotection, purification, and formulation methods.
• Operate, maintain, and troubleshoot HPLC, LC‑MS, and UV‑Vis instrumentation.
• Design and refine analytical methods for identity, purity, concentration, stability, and other 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.
• Develop scalable, reproducible synthesis and purification workflows.
• Establish effective quality control practices.
• Maintain laboratory equipment and coordinate servicing.
• Manage inventory of oligonucleotide sequences, reagents, and supplies.
• Maintain clear, accurate, and timely experimental documentation.
• Collaborate closely with biology, DMPK, and translational science teams.

• BS in Chemistry or related discipline with 5+ years of experience, or MS with 2+ years of industry experience.
• Hands‑on experience in oligonucleotide synthesis and purification.
• Proficiency with automated oligonucleotide synthesizers.
• Strong experience with HPLC, LC‑MS, and UV‑Vis.
• Experience preparing dosing solutions for in vitro/in vivo studies is a plus.
• Familiarity with laboratory automation and 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 team collaboration.

• Enjoy building systems, not just operating them.
• Take ownership of outcomes.
• Comfortable working with evolving priorities.
• Proactively identify problems and propose solutions.
• Maintain high standards of scientific rigor, integrity, and lab safety.

• Competitive base and equity compensation commensurate with experience.
• 401(k) company match.
• Generous medical, dental, and vision coverage with 100% premiums and deductibles covered.
• Company‑paid disability (STD, LTD) and life insurance.
• Paid parental leave.
• Family planning support up to $45,000.
• Unlimited paid time off and flexible schedules.
• Annual stipend for continuing education and individualized professional development.
• Wellness and extensive Employee Assistance Program.

Estimated annual base salary range: $80,000 – $95,000, plus equity compensation. Final offer will be based on experience and fit.

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 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.