Research Associate - Oligonucleotide Chemistry

Alloy TherapeuticsWaltham, MA
$65,000 - $80,000Hybrid

About The Position

We are seeking a highly motivated Research Associate to join our Nucleic Acid Chemistry team. The successful candidate will contribute to the synthesis, purification, formulation, and analytical characterization of modified oligonucleotides supporting discovery and early development programs. Working in a fast-paced startup environment, the successful candidate will contribute to established workflows while developing expertise in oligonucleotide synthesis technologies, purification methods, and analytical characterization. This role offers significant opportunities for technical growth and increasing scientific responsibility.

Requirements

  • BS in Chemistry, Biochemistry, Chemical Biology, Pharmaceutical Sciences, or a related discipline with 1-3 years of relevant industry or academic research experience, or MS in a related discipline with 0–2 years of relevant experience.
  • Hands-on laboratory experience with oligonucleotide synthesis, purification, analytical characterization, or related nucleic acid chemistry.
  • Familiarity with automated oligonucleotide synthesizers (e.g., Mermade or equivalent).
  • Basic understanding of phosphoramidite oligonucleotide synthesis chemistry.
  • Strong laboratory, troubleshooting, organizational, and documentation skills.
  • Excellent communication skills and the ability to work effectively in a collaborative, fast-paced environment.

Nice To Haves

  • Experience with common oligonucleotide analytical techniques, including HPLC, gel electrophoresis, UV quantification, and LC-MS (preferred), is highly desirable.
  • Experience with AKTA purification systems, ion-pair reverse-phase (IP-RP) or ion-exchange (IEX) chromatography.
  • Experience with chemically modified oligonucleotides and/or oligonucleotide conjugation.
  • Familiarity with laboratory automation or liquid handling systems.

Responsibilities

  • Perform synthesis, deprotection, purification, formulation, and characterization of modified oligonucleotides using automated synthesizers and established protocols.
  • Operate analytical instrumentation including HPLC, LC-MS, UV-Vis spectrophotometers, gel electrophoresis, and AKTA purification systems.
  • Analyze experimental data to determine identity, purity, concentration, yield, and other critical quality attributes.
  • Assist in troubleshooting and optimizing synthesis, purification, and analytical methods.
  • Prepare oligonucleotide materials for in vitro and in vivo studies.
  • Maintain accurate experimental records, laboratory inventory, and equipment.
  • Follow laboratory safety practices and contribute to SOP development and continuous process improvement.
  • Collaborate with scientists across chemistry, biology, DMPK, and analytical sciences to support research objectives.

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
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