Oligo extinction coefficient calculator (ε260)
Maintained by the Talindrew team · Last updated
An oligo's extinction coefficient at 260 nm is computed by the nearest-neighbor method: sum the pairwise dinucleotide coefficients and subtract the internal monomers, ε260 = Σε(pairs) − Σε(internal bases). Concentration then follows Beer–Lambert: c(µM) = A260 × 10⁶ / ε. This is the method IDT uses, so values match OligoAnalyzer exactly.
Result
ε260 by the nearest-neighbor method (Cantor, Warshaw & Shapiro 1970; Cavaluzzi & Borer 2004): the same method IDT OligoAnalyzer uses, so values should match it exactly. c = A260/ε; MW per OligoCalc (Kibbe 2007).
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What it looks like
Formula
ε260 = Σ ε(dinucleotides) − Σ ε(internal monomers) · c (µM) = A260 × 10⁶ / ε
Source: Cantor, Warshaw & Shapiro 1970; recommended by Cavaluzzi & Borer, NAR 2004
MW (g/mol) = Σ nucleotide MW − 61.96
Worked example
Given: dT₂₀ (twenty thymidines), A260 = 1.0 in 1 ml
- 1.19 TT dinucleotide pairs: 19 × 16,800 = 319,200.
- 2.Subtract 18 internal T monomers: 18 × 8,700 = 156,600.
- 3.ε260 = 319,200 − 156,600 = 162,600 M⁻¹cm⁻¹.
- 4.c = 1.0 × 10⁶ / 162,600 = 6.15 µM → 6.15 nmol per OD in 1 ml.
ε260(dT₂₀) = 162,600 M⁻¹cm⁻¹; 1 OD = 6.15 nmol
How the calculation flows
Units & constants
| Method | Nearest-neighbor (not base composition): accounts for stacking hypochromicity |
|---|---|
| Monomer ε (M⁻¹cm⁻¹) | dA 15,400 · dC 7,400 · dG 11,500 · dT 8,700 |
| Agreement | Matches IDT OligoAnalyzer (same method and tables) |
| vs flat A260 factor | More accurate than the '33 µg/ml per OD' average for any specific oligo |
| Assumes | Single-stranded, unmodified DNA at neutral pH, 25 °C |
| Price | Free |
Why not just use 33 µg/ml per A260 unit?
The flat factor is an average over all sequences. Real oligos deviate substantially: a pyrimidine-rich 20-mer and a purine-rich one can differ in true ε by 40%, which propagates directly into every downstream concentration. The nearest-neighbor calculation costs nothing and removes that error: it is what every oligo vendor prints on the spec sheet.
How do you quantify a primer stock from one A260 reading?
Dilute an aliquot so A260 falls between 0.1 and 1.0, measure, then divide by ε and multiply by the dilution factor and 10⁶ to get µM. The nmol-per-OD figure this page reports is the standard way vendors state yield: it is the nanomoles present in 1 ml of solution whose A260 reads 1.0.
What about modified oligos?
Fluorophores, quenchers and other 5′/3′ modifications absorb at 260 nm too. Add the modification's ε260 (from the vendor's datasheet) to the DNA value calculated here. IDT publishes per-modification contributions. Ignoring a fluorescein (ε260 ≈ 21,000) on a short probe overstates its concentration by 10–20%.
Frequently asked questions
This page uses the same nearest-neighbor tables and method as IDT OligoAnalyzer. Tools that estimate ε from base composition alone (Σ monomers, no stacking correction) run 5–10% high because they ignore hypochromicity.
Yes: duplex formation is hypochromic, lowering absorbance ~20–30%. These coefficients are for single strands (the state in which oligos are quantified). Quantify before annealing.
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