Associate Scientist​/Principal Associate Scientist - Oligonucleotide Chemistry

Principal Research Associate, Associate Scientist, or Principal Associate Scientist

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 a 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…