Is there a free primer melting temperature (Tm) calculator?

Yes. The 37degrees Tm + Restriction Mapper is free and runs in your browser. It calculates primer melting temperature with the nearest-neighbor model and maps restriction sites across the common cloning enzymes on both strands.

How is primer melting temperature calculated?

This tool uses the nearest-neighbor thermodynamic model (SantaLucia 1998) with a salt correction, which is more accurate than simple GC-content rules because it accounts for the specific sequence of adjacent base pairs.

Can it map restriction enzyme sites?

Yes. Paste a DNA sequence and the tool maps recognition sites for the common cloning enzymes across both strands, for linear or circular sequences — useful for planning digests and checking for unwanted cut sites.

Tm + Restriction Mapper: free primer melting temperature & restriction sites

Two calculations every bench molecular biologist repeats

What’s the Tm of this primer? Does this enzyme cut my insert, and where? Both are quick to answer and both usually mean a vendor login or a clunky applet. This widget does them in the browser — nothing uploaded, no account.

Use it now

Found a bug or want a feature? Tell us — we read everything.

Melting temperature

The headline number is the nearest-neighbor Tm using the SantaLucia (1998) unified parameters with a Na⁺ salt correction — the model primer-design tools rely on. Set your primer concentration and salt; the tool also shows the quick Wallace (2+4) and Marmur/GC% estimates for comparison, plus length, GC %, molecular weight, and the underlying ΔH / ΔS / ΔG₃₇.

For the M13 forward primer at 250 nM / 50 mM Na⁺ it returns ~51.6 °C, in line with published values. Mg²⁺ isn’t modeled (Na⁺ correction only), so treat the number as a monovalent-salt estimate.

Restriction-site mapper

Paste a sequence, pick linear or circular, and the tool maps the common cloning enzymes against it — on both strands, honoring IUPAC degeneracy. You get:

a one-line breakdown — how many enzymes cut, how many are single cutters, how many don’t cut;
single-cutter chips (the ones useful for linearizing a plasmid);
a sortable table of enzyme, recognition site (with the cut position marked), number of cuts, and 1-based positions;
a site map that labels the single cutters along the sequence.

Hit “Try example” to load a pUC19 multiple-cloning-site fragment and see the classic single cutters (EcoRI, SacI, KpnI, BamHI, XbaI, SalI, PstI, SphI, HindIII) line up.

Embed it on your site

<link rel="stylesheet" href="https://www.37degrees.io/interactive-tools/tm-restriction/styles.css" />

<div id="tm-widget-embed"></div>

<script>
  // Optional: window.TM_THEME = "light";
</script>
<script src="https://www.37degrees.io/interactive-tools/tm-restriction/widget.js"></script>

Free for typical research use. Heavy / production use? Get in touch.

Credits

Nearest-neighbor thermodynamics: SantaLucia, PNAS 1998. Restriction-enzyme recognition data derived from REBASE (Roberts et al.), free to use with attribution. Built and maintained by 37degrees — no third-party libraries, no data leaves the browser.