Why Bring Oligonucleotide Synthesis In-House? Benefits, Risks, and ROI

Introduction

Oligonucleotides are foundational to modern life science research — from PCR and sequencing to diagnostics and therapeutics. As demand grows, many labs are asking a critical question: does it make sense to bring oligonucleotide synthesis in-house?

While outsourcing remains common, in-house synthesis offers compelling advantages in speed, cost control, and IP protection. At the same time, it introduces new operational considerations. This post breaks down the real pros and cons to help you decide whether in-house oligo synthesis is right for your organization.

The Benefits of In-House Oligonucleotide Synthesis

1. Supply Chain Security
Relying on external vendors exposes labs to shipping delays, shortages, and geopolitical disruptions. In-house synthesis reduces dependency on third parties and gives teams greater control over timelines.

2. Faster Turnaround Times
Internal production enables same-day or next-day oligo availability — a major advantage for time-sensitive research and rapid iteration cycles.

3. Intellectual Property Protection
Keeping oligo production internal minimizes the risk of exposing proprietary sequences, especially in competitive or pre-publication research environments.

4. Long-Term Cost Control
While upfront investment exists, eliminating per-order outsourcing costs can significantly reduce expenses over time, particularly for high-volume labs.

5. Customization and Quality Control
In-house teams can fine-tune synthesis parameters, introduce custom modifications, and maintain direct oversight of quality standards.

The Challenges to Consider

Initial Capital Investment
Purchasing equipment, reagents, and lab infrastructure requires upfront budget allocation.

Space and Ventilation Requirements
Oligo synthesis uses organic solvents that require proper ventilation, solvent storage, and waste handling.

Operational Complexity
Successful synthesis demands expertise in organic chemistry, instrument maintenance, and reagent handling.

Regulatory and Safety Compliance
Permits, fire code compliance, and controlled substance regulations must be addressed.

Is In-House Synthesis Worth It?

For labs producing oligos regularly — especially at higher volumes or with specialized modifications — the long-term benefits often outweigh the challenges. The key is understanding your throughput needs, infrastructure readiness, and internal expertise.

👉 Next up: How oligonucleotide synthesizers actually work — and what it takes to run them.