Co-optimizing stability and activity in a DNA processing enzyme

gilishklar
Oct 28
2 min read

Updated: Nov 6

Scala’s stability design software improves activity and robustness of a DNA processing enzyme

In collaboration with:

Why it matters

DNA synthesis at scale depends on specialized enzymes that are stable and reliable under demanding conditions. Many DNA processing enzymes are dynamic, multi-domain proteins whose limited stability constrains performance in synthesis workflows. When Scala’s stability design software was applied to one such enzyme, the resulting variants were not only more stable but also showed marked improvements in activity - illustrating how Scala’s stability optimization can enhance overall DNA enzyme performance.

Problem

The DNA processing enzyme lacked sufficient stability, reducing its activity and limiting its use in production. Greater stability and robustness were required to make the enzyme suitable for advanced DNA synthesis applications.

What was done

In a single design round, Scala’s stability design software was applied to generate 47 variants of the enzyme, each carrying 9–38 mutations. These designs were experimentally tested by Ribbon Bio for expression, thermal stability, activity, and specificity.

Results

Design scope: one round generated 47 variants with 9–38 mutations each.
Expression: all variants were soluble and active; most expressed at higher yield than WT.
Catalytic efficiency: over 70% of variants showed ≥2× improvement, several up to ~5×.
Specificity: 93% of the designs exhibited enhanced substrate discrimination relative to WT

Impact

Stabilizing a dynamic, multi-domain enzyme not only improved its resilience but also enhanced its functional activity. By ensuring more of the enzyme remained correctly folded and active, Scala’s stability design software co-optimized stability and activity in a single round of design.

Data highlights

The EC₅₀ graph measures the enzyme concentration needed to reach half of maximum activity. Lower EC₅₀ values indicate greater catalytic efficiency. Most Scala-designed variants show 2–5× lower EC₅₀ than wild type, demonstrating that Scala's stability-guided design improved both folding and enzymatic performance in a single round.