Research Associate - Oligonucleotide Chemistry

alloytherapeutics; Waltham (MA); On-site; USD 65,000 - 80,000; Full time

Benefits offered by this job

Unlimited PTO

Education stipend

Wellness program / EAP

Job summary

Alloy Therapeutics in Waltham, MA is seeking a Research Associate for the Nucleic Acid Chemistry team to contribute to synthesis, purification, formulation, and analytical characterization of modified oligonucleotides for discovery and early development.

You will work in a fast-paced startup environment, expanding expertise in oligonucleotide synthesis technologies and analytical methods, with opportunities for growth and increased scientific responsibility.

Qualifications

• BS in Chemistry/Biochemistry/Chemical Biology or related, 1–3 years lab experience; MS with 0–2 years.
• Hands-on oligonucleotide synthesis, purification, and analytical characterization experience.
• Familiarity with automated oligonucleotide synthesizers (e.g., Mermade) and phosphoramidite chemistry.
• Strong documentation, troubleshooting, and collaborative skills.

Responsibilities

• Perform synthesis, deprotection, purification, formulation, and characterization of modified oligonucleotides.
• Operate analytical instruments (HPLC, LC-MS, UV, gel, AKTA) and analyze data.
• Prepare materials for in vitro and in vivo studies.
• Maintain records, inventory, and safety practices.
• Collaborate across chemistry, biology, DMPK, and analytical sciences.

Job description

Role Location: Waltham, MA

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 has evolved from a startup into a global biotechnology infrastructure company operating 11 divisions across 5 research sites in 4 countries on 3 continents. Our model - Integrated Independence - combines centralized capabilities with entrepreneurial operating divisions. 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.

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 Role

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 successful candidate will contribute to established workflows while developing expertise in oligonucleotide synthesis technologies, purification methods, and analytical characterization. This role offers significant opportunities for technical growth and increasing scientific responsibility.

Key Responsibilities

• 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

Required Qualifications

• 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.

Desirable Qualifications

• Experience with common oligonucleotide analytical techniques, including HPLC, gel electrophoresis, UV quantification, and LC‑MS (preferred), is highly desirable.
• 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.

What Will Make You Successful Here

• 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.

Taking Care of Our People

We support the individuality of what people need to do outside of work to empower them to do their best at work. While you focus on making better medicine together, we focus on programs and benefits that support a diverse and growing team. Whether you’re single, in a growing family, or nearing retirement, Alloy offers a variety of comprehensive and competitive benefits starting from day one.

Compensation

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

Health & Family

• 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)

Unique Perks

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

Pay Transparency

At Alloy Therapeutics, we believe in fostering trust and open communication. For this role, the estimated range is $65,000 - $80,000, with the final offer based on factors like your experience, skills, and alignment with our needs.

Additionally, this role is eligible for equity compensation, reflecting our commitment to shared success as we work together to make better medicines.

We are proud to offer competitive compensation and benefits, aiming to support our team’s professional and personal well‑being. If you have any questions about pay or benefits, we’re here to help.

Equal Opportunity Statement

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 [e-mail]. We will make every effort to respond to your request for disability assistance as soon as possible.