CRISPR
Silent PAM Destroyer
Remove unwanted PAMs with silent mutations to lock in your edit.
Design silent mutations that break PAMs and stop re-cutting while preserving protein sequence inside Helix Studio, the Genome IDE for editing.
System of Record →Section 1
What the tool is
The Silent PAM Destroyer finds codon-safe substitutions that disrupt PAMs without changing the amino acid sequence.
Section 2
Why scientists care
After HDR or Prime edits, remaining PAMs can trigger re-cutting and mixed populations.
Section 3
How Helix solves it
Codon table-aware swaps that break PAM motifs while keeping protein sequence
Section 4
How the algorithm works
We evaluate all codon substitutions that disrupt the PAM motif, ranking by synonymous preference and model implied mRNA stability.
Section 5
Try it in Helix Studio
Select the PAM to disable, review suggested silent swaps, and apply the edit to your design.
Section 6
FAQ
Does this alter amino acid sequence?
No—suggestions are synonymous unless you explicitly allow conservative substitutions.
Can I chain this with HDR donors?
Yes—Helix can embed the silent PAM destroyer into your HDR template automatically.
Do you support non-coding regions?
We surface motif-safe swaps for non-coding contexts where applicable.