Alloy Therapeutics

Associate Scientist/Principal Associate Scientist - Oligonucleotide Chemistry

Alloy Therapeutics • $80K — $110K *
Waltham, MA 02453In-Person
Pharmaceuticals & Biotech
Less than 5 years of experience
2 weeks ago
Job Overview by Ladders

Qualifications

  • BS in Chemistry or related field with 6+ years of industry experience, or MS with 4+ years.
  • Extensive hands-on experience in oligonucleotide synthesis and purification.
  • Proficient in using automated oligonucleotide synthesizers like Mermade, Dr. Oligo.
  • Strong expertise in HPLC, LC-MS, UV-Vis, and chromatographic techniques.
  • Experience with modified oligonucleotides and conjugation chemistry is desirable.
  • Familiarity with laboratory automation is a plus.
  • Excellent troubleshooting and data analysis skills.

Responsibilities

  • Independently design and optimize oligonucleotide synthesis using automated platforms.
  • Develop and troubleshoot purification workflows with AKTA Pure and HPLC.
  • Create analytical methods using HPLC, LC-MS, and other techniques to assess quality attributes.
  • Analyze experimental results to guide project decisions.
  • Prepare oligonucleotide materials for in vitro and in vivo studies.
  • Contribute to establishing laboratory infrastructure and best practices.
  • Mentor junior scientists and research associates.

Benefits

  • Generous medical, dental, and vision insurance with 100% premium coverage.
  • Company-paid disability and life insurance benefits.
  • Paid parental leave and family planning support.
  • Unlimited PTO and flexible schedules for work-life balance.
  • Annual professional development stipend and wellness programs.
Full Job Description
Role Location: Waltham, MA

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.

About Alloy Therapeutics

Alloy Therapeutics is a biotechnology company that develops novel antibody therapeutics using its proprietary drug discovery platform. The company's platform combines advanced computational algorithms with high-throughput screening technologies to identify and optimize therapeutic antibodies for a wide range of diseases. Alloy Therapeutics' customers include pharmaceutical and biotechnology companies, who use the company's platform to accelerate their drug discovery programs. The company was founded in 2017 and is headquartered in Cambridge, Massachusetts.
Learn more about Alloy Therapeutics
Size
50 employees
Industry
Pharmaceuticals & Biotech
Founded
2017
* Ladders Estimates

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