Scientific Operations Manager / Associate Scientist, Oligonucleotide Synthesis & Analytical Sciences

Job overview

The Scientific Operations Manager / Associate Scientist, Oligonucleotide Synthesis & Analytical Sciences role is onsite in Waltham, MA. The stated estimated salary range is $100,000–$125,000 per year, with equity eligibility. The role supports Alloy Therapeutics’ nucleic acid chemistry team and its oligonucleotide design-make-test cycle. The position combines operational management with hands-on laboratory chemistry to bring structure, traceability, and reliable execution to oligonucleotide research. It contributes to the team’s ability to design, synthesize, purify, test, and release sequences while improving operational visibility and quality practices.

What you'll do

• Manage sequence request intake, demand planning, scheduling, queue prioritization, and status reporting
• facilitate tier-board operations and track KPIs
• administer and optimize Benchling and related systems
• manage inventory and instrument readiness
• lead deviation investigations and CAPAs
• perform or develop into oligonucleotide synthesis, cleavage, deprotection, purification, analytical QC, documentation, method development, and process optimization.

What we're looking for

Skills & competencies

scientific operations manager

associate scientist

oligonucleotide synthesis

analytical sciences

alloy therapeutics

waltham ma

biotechnology

nucleic acid chemistry

laboratory operations

benchling

hplc

lc-ms

$100k-$125k/year

equity eligible

Work arrangement

• Weekend coverage required

Benefits & perks

• Equity compensation, 401(k) company match, medical, dental and vision benefits with premiums and deductibles covered, company-paid disability and life insurance, paid parental leave, family-planning support up to $45,000, unlimited PTO, flexible schedules, continuing-education stipend, and employee assistance resources.

Why this role

Approximately 50/50 split between operational management and hands-on laboratory work; oligonucleotide experience is not required, and training on the synthesis platform and analytical methods is offered.

About the employer

Alloy Therapeutics is hiring for this role. Industry: Research and Development in Biotechnology (except Nanobiotechnology). Sector: 54.