How is the nearest-neighbor Tm calculated?

Using SantaLucia (1998) unified nearest-neighbor ΔH/ΔS parameters, with an entropy salt correction for Na⁺ and a monovalent-equivalent for Mg²⁺ (corrected for dNTP chelation). It is more accurate than the Wallace or salt-adjusted formulas, especially for primer-length oligos.

What counts as a problematic dimer or hairpin?

A more negative ΔG means a more stable structure. As a rough guide, ΔG below about −6 kcal/mol is worth attention, and any structure that involves the 3′ end is the most likely to interfere with extension. These are screening estimates — confirm critical designs with a dedicated folding tool.

Can I analyze many oligos at once?

Yes. Batch mode accepts one oligo per line, FASTA, or “name,sequence” rows, computes Tm, GC, ΔG and structure for each, and exports a CSV.

Oligo Analyzer — Nearest-Neighbor Tm, Primer Dimers & Hairpins

Nearest-neighbor Tm, ΔG, hairpins and primer dimers for any oligo or primer pair.

🔒 Local processing — pasted sequences are not uploaded

Analyze a primer or oligo the way a thermodynamics calculator does: a nearest-neighbor melting temperature (Tm) based on SantaLucia 1998 parameters, the underlying ΔH/ΔS/ΔG, and screening for hairpins, self-dimers and cross-dimers between a primer pair. Adjust the oligo, Na⁺, Mg²⁺ and dNTP concentrations to match your reaction, and run a whole list of oligos at once in batch mode with CSV export — no signup required.

Reaction conditions

Oligo (nM)Na⁺ (mM)Mg²⁺ (mM)dNTP (mM)

Oligo / primer sequence (5′→3′)

0 nt

Tm uses SantaLucia (1998) nearest-neighbour thermodynamics with a salt correction for Na⁺ and a monovalent-equivalent for Mg²⁺/dNTP. Hairpin and dimer ΔG are screening estimates — confirm critical designs with a dedicated secondary-structure tool. A 3′-end dimer/hairpin is the most likely to disrupt PCR.

How to use the Oligo Analyzer tool

1Pick a mode: a single oligo, a forward/reverse primer pair, or a batch list.
2Paste the sequence(s) and set the reaction conditions (or use a preset).
3Read the nearest-neighbor Tm and ΔG, and check the hairpin / dimer panels — a 3′-end structure is the most likely to disrupt PCR.

Frequently asked questions

How is the nearest-neighbor Tm calculated?: Using SantaLucia (1998) unified nearest-neighbor ΔH/ΔS parameters, with an entropy salt correction for Na⁺ and a monovalent-equivalent for Mg²⁺ (corrected for dNTP chelation). It is more accurate than the Wallace or salt-adjusted formulas, especially for primer-length oligos.
What counts as a problematic dimer or hairpin?: A more negative ΔG means a more stable structure. As a rough guide, ΔG below about −6 kcal/mol is worth attention, and any structure that involves the 3′ end is the most likely to interfere with extension. These are screening estimates — confirm critical designs with a dedicated folding tool.
Can I analyze many oligos at once?: Yes. Batch mode accepts one oligo per line, FASTA, or “name,sequence” rows, computes Tm, GC, ΔG and structure for each, and exports a CSV.

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