Associate Scientist/Principal Associate Scientist - Oligonucleotide Chemistry

Alloy Therapeutics • Waltham, MA

7d • $80,000 - $110,000 • Hybrid

About The Position

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.

Requirements

• 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.

Nice To Haves

• 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.

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.

Benefits

• 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 (e.g., IVF/PGT, adoption, surrogacy, egg retrieval)
• 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

What This Job Offers

• Job Type: Full-time
• Career Level: Mid Level