Research Associate - Oligonucleotide Chemistry

Role Location

Waltham, MA

Alloy Therapeutics is a biotechnology ecosystem company that empowers the global scientific community to make better medicines together.

We are seeking a highly motivated Research Associate to join our Nucleic Acid Chemistry team. The successful candidate will contribute to the synthesis, purification, formulation, and analytical characterization of modified oligonucleotides supporting discovery and early development programs. Working in a fast‑paced startup environment, the candidate will develop expertise in oligonucleotide synthesis technologies, purification methods, and analytical characterization while contributing to established workflows.

• Perform synthesis, deprotection, purification, formulation, and characterization of modified oligonucleotides using automated synthesizers and established protocols.
• Operate analytical instrumentation including HPLC, LC‑MS, UV‑Vis spectrophotometers, gel electrophoresis, and AKTA purification systems.
• Analyze experimental data to determine identity, purity, concentration, yield, and other critical quality attributes.
• Assist in troubleshooting and optimizing synthesis, purification, and analytical methods.
• Prepare oligonucleotide materials for in‑vitro and in‑vivo studies.
• Maintain accurate experimental records, laboratory inventory, and equipment.
• Follow laboratory safety practices and contribute to SOP development and continuous process improvement.
• Collaborate with scientists across chemistry, biology, DMPK, and analytical sciences to support research objectives.

• BS in Chemistry, Biochemistry, Chemical Biology, Pharmaceutical Sciences, or a related discipline with 1‑3 years of relevant industry or academic research experience, or MS in a related discipline with 0‑2 years of relevant experience.
• Hands‑on laboratory experience with oligonucleotide synthesis, purification, analytical characterization, or related nucleic acid chemistry.
• Familiarity with automated oligonucleotide synthesizers (e.g., Mermade or equivalent).
• Basic understanding of phosphoramidite oligonucleotide synthesis chemistry.
• Strong laboratory, troubleshooting, organizational, and documentation skills.
• Excellent communication skills and the ability to work effectively in a collaborative, fast‑paced environment.

• Experience with common oligonucleotide analytical techniques, including HPLC, gel electrophoresis, UV quantification, and LC‑MS (preferred).
• Experience with AKTA purification systems, ion‑pair reverse‑phase (IP‑RP) or ion‑exchange (IEX) chromatography.
• Experience with chemically modified oligonucleotides and/or oligonucleotide conjugation.
• Familiarity with laboratory automation or liquid handling systems.

• Passion for hands‑on laboratory research and learning new technologies.
• Strong attention to detail and commitment to generating high‑quality scientific data.
• Curiosity and initiative in solving technical challenges.
• Ability to adapt to changing priorities in a dynamic startup environment.
• Commitment to scientific integrity, teamwork, and laboratory 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.
• Unlimited PTO and flexible schedules.
• Annual stipend for continuing education with a commitment to your career through an individualized professional development plan.
• Wellness and extensive Employee Assistance Program (EAP) resources for mental wellness.

Pay Transparency:
For this role, the estimated range is $65,000 - $80,000, with the final offer based on factors such as experience, skills, and alignment with our needs. This role is also 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.