TSDR Probe Designer — toehold exchange probes for SNP genotyping

Designs a two-strand toehold exchange probe (Complement C + Protector P) for a target you supply with the variant site marked as [A/G] (an SNP), [/ATG] (an insertion) or [ATG/] (a deletion); IUPAC codes such as [R] also work. The Protector length and toehold are tuned so the displacement reaction is near-thermoneutral (ΔG°_rxn ≈ 0) for the on-target allele, which maximises discrimination of SNPs and short indels.

Method: Zhang, Chen & Yin (Nat Chem 2012); kinetics scale with toehold ΔG per Zhang & Winfree (JACS 2009). First-pass build: equilibrium thermodynamics only (not a kinetic simulation); mismatch penalties are approximate — see the Warnings tab.

Target sequence (5′→3′), variant marked [A/G], [/ATG] or [ATG/]:

Design parameters

Probe (C) conc. (µM)

Target (X) conc. (µM)

Operating T (°C)

Target ΔG°_rxn (kcal/mol)

Total salt Na⁺/K⁺ (mM)

Mg²⁺ (mM)

Probe footprint (nt)

Toehold length range (nt)

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Two-colour mode (one probe per allele)

Need details? Markup, parameters and the thermoneutral-design rationale are documented in Help: TSDR tool.
Export: click inside a result area → Ctrl+A → Ctrl+C.