Associate Scientist, Oligonucleotide Chemistry

alloytherapeutics; Waltham (MA); On-site; USD 80,000 - 110,000; Full time

Benefits offered by this job

Unlimited PTO

Continuing education stipend

Wellness and EAP

401(k) company match

Equity compensation

Job summary

Alloy Therapeutics in Waltham, MA is seeking a Principal Research Associate or Associate Scientist to join the Nucleic Acid Chemistry team. You will lead synthesis, purification, formulation, and analytical characterization of modified oligonucleotides to support discovery and early development programs.

In a fast-paced startup environment, you will design experiments, optimize processes, and develop new technologies while mentoring junior scientists and collaborating with chemistry, biology,

Qualifications

• BS in Chemistry or related field with 6+ years of industry experience, or MS with 4+ years.
• Hands-on oligonucleotide synthesis, purification, and analytical characterization.
• Experience with automated oligonucleotide synthesizers (Mermade, Dr. Oligo, AKTA Oligopilot).
• Strong HPLC, LC-MS, UV-Vis experience and purification techniques.
• Experience with modified oligos and conjugation chemistries (GalNAc, lipids, PEG).
• Experience preparing oligonucleotide materials for biological studies.
• Excellent troubleshooting, design, data analysis, and mentoring skills.

Responsibilities

• Design, execute, and optimize synthesis of modified oligonucleotides on automated platforms.
• Develop, optimize, and troubleshoot deprotection, purification, formulation, and conjugation workflows.
• Design and optimize analytical methods (HPLC, LC-MS, UV-Vis, gel) for quality attributes.
• Analyze, interpret, and communicate results to guide project decisions.
• Prepare oligonucleotide materials for in vitro and in vivo studies.
• Develop scalable, robust synthesis and purification processes.
• Establish laboratory infrastructure, SOPs, and quality systems.
• Maintain, troubleshoot, and oversee instrumentation and preventive maintenance.
• Manage laboratory inventory and reagents.
• Document experiments and present findings in reports and presentations.
• Collaborate with chemistry, biology, DMPK, analytics, and translational teams.
• Mentor junior scientists and promote scientific best practices.

Skills

Oligonucleotide synthesis

Purification

Analytical characterization

Process optimization

Automated synthesizers

HPLC

LC-MS

Conjugation chemistry

Laboratory automation

Troubleshooting

Project management

Communication

Education

BS in Chemistry

MS in Chemistry

Tools

Mermade

Dr. Oligo

AKTA Oligopilot

AKTA Pure

Job description

Alloy Therapeutics in Waltham, MA is seeking a Principal Research Associate or Associate Scientist to join the Nucleic Acid Chemistry team. You will lead synthesis, purification, formulation, and analytical characterization of modified oligonucleotides to support discovery and early development programs.

In a fast-paced startup environment, you will design experiments, optimize processes, and develop new technologies while mentoring junior scientists and collaborating with chemistry, biology,