DNA Calculator

[Na⁺] /mM: [Mg²⁺] /mM: [dNTPs] /mM: [Primer] /nM^†:
^†When primer and target DNA are in equal concentration, input 1/2 [primer]_initial (1/4 [total oligonucleotides]_initial). Otherwise input [Primer]_initial - 1/2[Target DNA]_initial

5'- Sequence -3'

Abs. @ 260 nm

Input one sequence per row.
"Abs." is used only for concentration calculations.
The mw value is calculated with the 5' end as -OH.
By bookmarking the search results URL, the sequence information you entered will be preserved.
The condition where "SantaLucia's (1996)" values and **DO NOT** "Use traditional formula" is more reliable, but some PCR reagents uses "Breslauer's (1986)" and "traditional formula".
An Excel version is also available on GitHub.

Values used for calculation

	pdA	pdC	pdG	pdT	dApdA	dApdC	dApdG	dApdT	dCpdA	dCpdC	dCpdG	dCpdT	dGpdA	dGpdC	dGpdG	dGpdT	dTpdA	dTpdC	dTpdG	dTpdT
ε_260,ss	15400	7400	11500	8700	27400	21200	25000	22800	21200	14600	18000	15200	25200	17600	21600	20000	23400	16200	19000	16800
ΔH° /kcal･mol^-1
ΔS° /cal･mol^-1K^-1

	A	C	G	T
Mw	313.21	289.18	329.21	304.2
Mw (ds)	617.41	618.39	618.39	617.41

Formula

Use traditional formula for Tm

ɛ_{260, ss} = \sum_{i = 1}^{N_{b} - 1} ɛ_{i, i + 1} - \sum_{i = 2}^{N_{b} - 1} ɛ_{i}

ɛ_{260, ds} = (1 - h) (ɛ_{260, ss} + ɛ_{260, ss (rev)})

h = (0.059 \times {Count}_{GC} + 0.278 \times {Count}_{AT}) / Length

where

ɛ_{i, i + 1}

are the extinction coefficients for doublets of nucleotides,

ɛ_{i}

is the extinction coefficient for the nucleotide i, and

N_{b}

is the number of nucleotides in the oligomer sequence^[4].

T_{m} = {Δ H}^{\circ} \div ({Δ S}^{\circ} + R \ln C_{T}) = 1000 \times \sum_{i = 1}^{N_{b} - 1} {Δ H}^{\circ}_{i, i + 1} \div (Initial S + \sum_{i = 1}^{N_{b} - 1} {Δ S}^{\circ}_{i, i + 1} + 1.987 \ln [Primer]) + 16.6 \log_{10} [{Na}^{+}] - 273.15

where R is gas constant (= 1.987 kcal/(K･mol)), C_T is total oligonucleotide concentration, Initial S is -10.8 or -9.0 (Sugimot's value), and ∂T_m/∂log[Na⁺] = 16.6 °C^{[1, 2, 3]}.
The effects of magnesium ions and dNTPs were represented as an effective sodium ion concentration, calculated according to the following equation^[5].

[{Na}^{+} (eq)] = [{Na}^{+}] + 120 \times \sqrt{[{Mg}^{2 +}] - [dNTPs]}

DNA Calculator

Values used for calculation

Formula

References