Design PCR primers by target Tm or primer length, with optional restriction enzyme overhangs and primer-quality checks.
PCR Primer Designer is a browser-based tool for designing forward and reverse primers from a DNA template; generated pairs can go straight to Primer Binding Checker in the connected browser workflow.
Use note: Choose fixed primer length or target melting temperature first; add restriction enzyme overhangs only after the annealing parts look clean.
Accepted file types: .txt, .fa, .fasta, .fna, .ffn, .seq, .gb, .gbk, .genbank. SnapGene .dna files are not yet supported; export as FASTA or GenBank.
Transfer the current validated sequence to another Mol Biology Tools page in a new tab.
Leave amplicon region blank to use the full sequence. Circular templates can use ranges that cross base 1, such as 4800-250. Enter either primer length or target Tm.
Each primer accepts one restriction site only. Search by enzyme name or recognition sequence, or type one exact DNA/IUPAC motif. Auto flanking uses built-in enzyme-specific rules with at least 3 bases; if no rule is available, it falls back to GCGC.