| name | tooluniverse-primer-design |
| description | PCR / qPCR primer and oligo design — design forward/reverse primers for a target region (SantaLucia nearest-neighbor thermodynamics), compute melting temperature (Tm) and annealing temperature (Ta), check GC content, and screen an oligo for hairpins and primer-dimers. Use when you need primers for a sequence, want to QC an existing primer pair, or need the Tm of an oligo. Covers the primer-design rules (Tm matching, GC clamp, 3'-end, length) and the tools' constraint quirks. |
| disable-model-invocation | true |
PCR / qPCR Primer & Oligo Design
Design primers for a target DNA region, get their Tm/Ta, and QC them for the secondary-structure problems that make a PCR fail.
When to use this
- Design a forward/reverse primer pair to amplify a region of a sequence.
- Compute the Tm / annealing temperature of a primer.
- QC an existing primer pair (GC clamp, 3'-end, hairpins, self/cross dimers, Tm match).
Step 1 — Design a primer pair
tu run DNA_primer_design '{"operation":"primer_design",
"sequence":"ATGGCG...AACGTG", # full template; must be >= target_end + flanking primer room
"target_start":40, "target_end":125,
"tm_target":60, "product_size_min":80, "product_size_max":140}'
Returns forward_primer / reverse_primer (sequence, tm, gc_content, length, position) and product_size. (target_end is clamped to the sequence length, so a too-short template silently shrinks the target — see the constraint quirk below.)
Constraint quirk — read this or it will error. is the region the , and the design only succeeds when that span fits inside the product-size window AND good-Tm primers can be placed flanking it. So you need roughly: , with enough flanking sequence on both sides. Common errors and the fix:
