Associate Scientist/Principal Associate Scientist - Oligonucleotide Chemistry

Job Description

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 Principal Research Associate, Associate Scientist, or Principal Associate Scientist to play a key role in expanding our oligonucleotide chemistry capabilities. The successful candidate will join our growing Nucleic Acid Chemistry team to lead and execute the 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. Depending on experience, the individual will be expected to progressively take ownership of experimental design, process optimization, and technology development in addition to executing established workflows.

Key Responsibilities

• Independently design, execute, and optimize synthesis of modified oligonucleotides using automated platforms (e.g., Mermade, Dr. Oligo, AKTA Oligopilot).
• Develop, optimize, and troubleshoot deprotection, purification using AKTA Pure and HPLC systems (reverse-phase, ion-exchange, SEC,), formulation, and conjugation workflows. 
• Design, develop, and optimize analytical methods using HPLC, LC-MS, UV-Vis, gel electrophoresis, and related techniques to assess identity, purity, concentration, stability, and other critical quality attributes.
• Analyze, interpret, and communicate experimental results to guide project decisions and improve process performance.
• Prepare and characterize oligonucleotide materials for in vitro and in vivo studies.
• Develop scalable, robust, and reproducible synthesis and purification processes to support research programs.
• Contribute to establishing laboratory infrastructure, SOPs, quality systems, and best practices appropriate for a growing R&D organization.
• Maintain, troubleshoot, and oversee laboratory instrumentation and coordinate preventive maintenance and vendor support.
• Manage laboratory inventory, critical reagents, consumables, and oligonucleotide materials.
• Maintain accurate experimental documentation and communicate findings through technical reports and presentations.
• Collaborate closely with chemistry, biology, DMPK, analytical, and translational research teams to advance program goals.
• Mentor junior scientists and research associates, providing technical guidance and promoting scientific best practices.

Qualifications

• BS in Chemistry or a related discipline with 6+ years of relevant industry experience, or MS with 4+ years of industry experience.
• Extensive hands-on experience in oligonucleotide synthesis, purification, analytical characterization, and process optimization.
• Demonstrated proficiency operating automated oligonucleotide synthesizers (e.g., Mermade, Dr. Oligo, AKTA Oligopilot, or equivalent).
• Strong expertise in HPLC, LC-MS, UV-Vis, and chromatographic purification techniques.
• Experience with modified oligonucleotides and conjugation chemistries (e.g., GalNAc, lipids, PEG, peptides) is highly desirable. 
• Experience preparing oligonucleotide materials for biological studies is preferred.
• Familiarity with laboratory automation (ex. liquid handling systems) is a plus.
• Excellent troubleshooting, experimental design, data analysis, and process development skills.
• Demonstrated ability to independently manage multiple projects in a fast-paced research environment.
• 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 developing new technologies and improving existing processes.
• You take ownership of scientific challenges and drive projects to completion.
• You proactively identify technical risks and develop practical solutions.
• You thrive in a collaborative, fast-paced startup environment with evolving priorities.
• You enjoy mentoring others and fostering scientific excellence.
• You maintain high standards of scientific rigor, data integrity, 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 $80,000 - $110,000, 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 View email address on ziprecruiter.com .  We will make every effort to respond to your request for disability assistance as soon as possible.

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