Principal Research Associate - Oligonucleotide Chemistry

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


In our fast-paced startup environment, this role requires strong technical skills, hands-on execution, problem-solving creativity, and a willingness to take ownership of processes and infrastructure as we scale.

Key Responsibilities

• 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.

Qualifications

• 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.

What Will Make You Successful Here

• 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.

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 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, 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.

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 [email protected]. We will make every effort to respond to your request for disability assistance as soon as possible.

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