The Enzyme Optimization Decision for Assay Developers: De novo or OTS tailoring?

Assay developers are often faced with two paths to optimize reagents and enzyme performance: engineering new reagents or using an off-the-shelf version and tailoring its specifications. Which is the better choice?

Our team specializes in optimizing enzymes and reagents for specific assay performance. When we talk with assay development scientists, we find most teams asking for “custom enzymes” are really asking for one of two things: 

1. A brand-new enzyme solution built around a specific performance target (de novo path), or
2. A proven enzyme that’s been tuned to match the realities of their workflow (tailored off-the-shelf “OTS” path).

These are different development paths and clarifying which one you need from the outset makes projects move faster and more cost-effectively. This is especially true when considering configuration requirements like lyophilization, ultra-low volumes, microfluidic cartridges, or tight QC requirements. 

When we talk with assay development scientists, we find most teams asking for “custom enzymes” are really asking for one of two things – 1) A brand-new enzyme solution (de novo) – or – 2) A proven enzyme that’s been tuned to match (tailored 0ff the shelf “OTS”)

 

Here is how we approach this decision.

Enzyme Optimization – De novo path

The de novo path starts from a defined performance target and works backward to reagents or enzyme structure. Development teams take this approach when an off-the-shelf enzyme, even with minor tweaks, cannot realistically meet the performance target such as sensitivity, inhibitor tolerance, speed, temperature profile, or long-term stability. De novo can mean utilizing a custom-designed sequence or engineered variant that must be expressed, purified, formulated, and scaled reproducibly. Alternatively, it can mean developing a new enzyme solution around proprietary chemistry. 

This path is best when enzyme behavior is a true differentiator and you’re willing to invest in development to get a step-change in performance.  If you are working with a fully proprietary reagent system where the enzymes or formulations are co-designed for the device, then de novo might be the better approach as you can trade performance in an area that you don’t need for an increase in an area that matters.

Enzyme Optimization – Tailored OTS path

The tailored off-the-shelf (OTS) path starts with existing, well-characterized reagents and optimizes the specifications to fit your product and manufacturing workflow. In many cases, teams will be starting with reagents they can purchase from a catalog. Common tailoring or customization levers include altering concentration or buffer compositions, using glycerol-free formats for lyophilization, changing packaging/fill volumes, and improving stability (likely by lyophilization). If your challenge is making what already works behave reliably under your specific conditions, tailoring an OTS enzyme is usually the smarter decision—and it can still deliver meaningful performance gains while reducing development risk and timeline.

Altering an OTS reagent is often the fastest route when baseline performance is acceptable, but the standard reagent format is not optimal. Choose the tailored OTS path when the bottleneck of the assay is format or device compatibility, and not the actual function of the reagents. If the reagents are working in the assay, only a little tweaking might be required to obtain optimal configuration.  Customization programs can move quickly and will often have lower technical risk. 

A practical comparison for choosing enzyme optimization development paths:

Timeline

• OTS: faster because the reproducible manufacturing processes and QC parameters are established and validated
• De novo: longer as development, reagent and enzyme optimization, and scale-up are part of the effort

Risk

• OTS: lower scientific risk; main risks are compatibility and stability
• De novo: higher technical and scale-up risk, offset by improved enzyme performance 

Differentiation

• OTS: lower scientific risk; main risks are compatibility and stability
• De novo: higher technical and scale-up risk, offset by improved enzyme performance

Regulated commercialization

Both paths can be commercialization-ready when manufacturing and documentation are handled under an ISO compliant or certified quality system and when established release specifications are tied to validated processing and assay performance.

The “best-of-both-worlds” strategy (often the winning approach)

Many teams start by tailoring an off-the-shelf enzyme to get a working formulation into verification and early validation studies. In parallel, they may pursue a de novo program if they need stronger differentiation for performance long-term. The key is to be explicit about which track has prioritization, because the development plan, data package, and timeline are distinctly different.

Development partners can bring your team valuable technical and manufacturing expertise.  From our experience, projects move quickly when there are: 

• Clear use cases (assay type, sample type, workflow)
• Defined configurations (buffer requirements, storage format, packaging sizes)
• Well characterized performance targets (what does “better” mean in measurable terms?)
• Set scale and quality expectations (R&D lots vs. OEM supply)

If you know the enzyme you need and the challenge is the “last mile” (format, stability, integration), start with OTS tailoring. If you need fundamentally new behaviors, something you can’t simply buy—de novo development is worth the investment.

 

Explore your enzyme optimization options – Contact Us

 

Table 1: Reagents and enzyme optimization development parameters comparing off-the-shelf (OTS) to de novo pathways