Oligo Molecular Weight Calculator - MW, OD260 & ε260

Calculate oligo MW, molecular weight, OD260, ε260 extinction coefficient, nmol, µg, and stock concentration conversions for DNA and RNA oligonucleotides. Use this single-metric workspace before dilution or full primer review.

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Length: 0 nt

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Enter a sequence and click"Calculate MW"

What Is Oligonucleotide Molecular Weight?

Molecular weight (MW) of an oligonucleotide is the sum of the atomic weights of all atoms in the molecule, typically expressed in Daltons (Da) or grams per mole (g/mol). For a single-stranded DNA oligonucleotide, MW depends on the sequence composition and any chemical modifications. A typical 20-mer DNA primer has a MW of approximately 6,000-6,500 Da.

Knowing the exact MW is essential for converting between mass (µg) and molar (nmol, pmol) concentrations — a critical step when preparing stock solutions from lyophilized oligos. Vendors typically report the amount of synthesized oligo in either OD260 units or nanomoles, and you need MW to convert between these units for accurate experimental concentrations.

The extinction coefficient (ε260) is equally important: it tells you how much UV light at 260 nm the oligo absorbs, allowing you to measure concentration using a spectrophotometer such as a NanoDrop. The calculator uses nearest-neighbor ε260 calculation for DNA sequences, which accounts for base stacking interactions instead of relying only on simple base-additive sums.

This page should stay a single-metric MW and OD260 workspace. When the same sequence also needs Tm, GC%, hairpin, self-dimer, hetero-dimer, mismatch, or BLAST review, open the Primer Analyzer for the full OligoAnalyzer-style report instead of using this page as an all-in-one analyzer.

How to Use the Molecular Weight Calculator

  1. Enter your oligonucleotide sequence (5' to 3') in the input field. Both DNA and RNA are supported.
  2. Select any 5' or 3' modifications (phosphate, biotin) if applicable.
  3. The calculator instantly displays: molecular weight (Da), extinction coefficient (ε260 in L/(mol·cm)), nmol/OD260, and µg/OD260.
  4. To convert from OD260 to concentration: enter the measured OD260 value and resuspension volume to get the concentration in µM and ng/µL.
  5. For batch processing, switch to Batch Mode and paste multiple sequences.

Frequently Asked Questions

How is oligonucleotide molecular weight calculated?
For single-stranded DNA, MW is calculated by summing the average molecular weights of each nucleotide residue (dAMP: 331.2, dCMP: 307.2, dGMP: 347.2, dTMP: 322.2 g/mol), subtracting one water molecule (18.02 g/mol) per phosphodiester bond, and adding the mass of any terminal modifications. The calculator performs this calculation automatically and accounts for 5'-hydroxyl vs 5'-phosphate terminal groups.
What is the extinction coefficient (ε260) and why does it matter?
The molar extinction coefficient (ε260) describes how strongly an oligonucleotide absorbs UV light at 260 nm. It is measured in L/(mol·cm) and used with Beer-Lambert law (A = εcl) to convert absorbance readings into concentration. The nearest-neighbor method for calculating ε260 accounts for hypochromicity — the reduction in UV absorption caused by base stacking in single-stranded oligos — making it significantly more accurate than simply summing individual nucleotide extinction coefficients.
How do I convert OD260 to nmol or µg?
Use the conversion factors: nmol = OD260 × (nmol/OD260 factor) and µg = OD260 × (µg/OD260 factor). The calculator provides both factors automatically. For example, a 20-mer with nmol/OD260 = 5.2 and µg/OD260 = 33: if you have 3.5 OD260, that equals 18.2 nmol or 115.5 µg of oligonucleotide. Divide by your resuspension volume to get concentration.
Does salt form affect molecular weight?
Yes. Oligos from vendors are typically supplied as sodium or ammonium salts. The sodium salt form adds approximately 22 Da per phosphodiester bond (one Na⁺ per negative charge). The calculator reports free-acid, non-salt MW by default. If your vendor reports salt-form MW, expect values approximately 5-7% higher than a free-acid calculation.
How accurate is the nearest-neighbor extinction coefficient?
The nearest-neighbor method for ε260 is accurate to within ±5% for most sequences. It accounts for base stacking hypochromicity, which can reduce the extinction coefficient by 10-30% compared to the sum of individual bases. The main limitation is for highly structured single-stranded sequences (strong hairpins), where additional hypochromicity from intramolecular base pairing can cause the actual ε260 to be 5-15% lower than predicted.
When should I use Primer Analyzer instead of this MW calculator?
Use this page when mass, molecular weight, OD260, extinction coefficient, or stock concentration is the only task. Use the Primer Analyzer when MW needs to be reviewed together with Tm, GC%, hairpins, self-dimers, hetero-dimers, mismatch effects, BLAST review, and client-side detailed primer output.

Related Tools

Dilution Calculator

After calculating MW, use the dilution calculator to prepare stock solutions and working concentrations.

Tm Calculator

Calculate melting temperature alongside MW for complete primer characterization.

Primer Analyzer

Use the Primer Analyzer when MW should be reviewed together with Tm, GC%, hairpins, dimers, and mismatch effects.

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Related reading

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