Primer Design

Primer Designer

Design primers for enzyme insertion, amino acid insertion, indels (amplify/delete a region), or gel-based insertion verification

Design Mode

Enzyme Insertion

Insert restriction enzyme recognition sites

Amino Acid Insertion

Insert amino acid sequences with homology arms

Indels (PCR)

Design PCR primers to amplify a region, or cut one out

Insertion Verification

Design genotyping PCR primers to confirm an insertion on a gel

DNA Sequence

Full DNA sequence in uppercase (A, T, C, G)

Insertion Position (1-based)

Position where insertion will occur

Select Enzyme

Only enzymes not already present in your sequence are shown

Your Enzymes (optional)

Paste enzyme names you own to filter the dropdown (e.g., EcoRI, BamHI). Matching enzymes will be shown first.

Insert Type

Choose whether the sequence below is amino acids (auto-converted to DNA) or DNA bases to insert directly, unchanged

Amino Acid Sequence

Single letter amino acid codes

Quick Insert (Motif Library)

Motifs are amino acid sequences -- only usable in Amino acid mode

Optional: Add Enzyme Site

Select Enzyme (optional)

Select an enzyme to also design primers for enzyme site insertion at the same position

Your Enzymes (optional)

Paste enzyme names you own to filter the dropdown (e.g., EcoRI, BamHI)

Operation

Amplify this region

Primers point inward, flanking the target region, to amplify it

Leave out this region

Primers point outward, back-to-back around the region, to cut it out

Target Region Sequence

The region to amplify. Must be an exact substring of the DNA sequence above.

Primer Placement

Start at region edges

Forward primer begins exactly where the region starts; reverse primer begins exactly where it ends

Allow tolerance

Both primers sit out in the flanking sequence, for leniency when confirming a correct insertion

In edge mode both primers sit exactly at the region boundaries; in tolerant mode both move outward by the same amount so a correct insertion still amplifies even if the exact junction isn't precise.

New here? Load an example to see how PEEK works.