Utilities
PCR Primer Designer for Genome Editing
Design PCR primers that align with CRISPR and Prime Editing assays.
Design PCR primers centered on CRISPR and Prime Editing assays with Tm/GC balance and QC in Helix Studio, the Genome IDE.
System of Record →Section 1
What the tool is
The PCR Primer Designer proposes primer pairs around your edit site with Tm/GC balance and amplicon size tuned for downstream analysis.
Section 2
Why scientists care
Generic primer tools ignore edit windows, leading to assays that miss the effect you care about.
Section 3
How Helix solves it
Adjustable amplicon spans centered on cuts or RTT windows
Section 4
How the algorithm works
Primer candidates are generated with constraint solving for Tm, GC, and amplicon size; problematic motifs are filtered out.
Section 5
Try it in Helix Studio
Choose your guide or pegRNA, set desired amplicon size, and select from QC-ranked primer pairs.
Section 6
FAQ
Can I include barcodes/adapters?
Yes—toggle adapters and Helix will account for them in Tm calculations.
Do you support multiplex panels?
We score cross-dimers and warn about overlapping amplicons before you finalize a panel.
How are primers delivered?
CSV/FASTA plus annotated PDFs ready for ordering.