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DNA and RNA Molecular Weight Calculator

Calculate the molecular weight of a single-stranded DNA, double-stranded DNA or RNA sequence from its base composition, with a choice of 5′ hydroxyl or phosphate end.

Formula

MW=∑nbase wresidue+H2O−HPO3\mathrm{MW} = \sum n_{\text{base}}\,w_{\text{residue}} + \mathrm{H_2O} - \mathrm{HPO_3}
5′ phosphate:MW=∑nbase wresidue+H2O\text{5}'\text{ phosphate:}\quad \mathrm{MW} = \sum n_{\text{base}}\,w_{\text{residue}} + \mathrm{H_2O}
MWdsDNA=MWstrand+MWcomplement\mathrm{MW}_{\text{dsDNA}} = \mathrm{MW}_{\text{strand}} + \mathrm{MW}_{\text{complement}}
wresiduew_{\text{residue}}
the nucleoside monophosphate less one water, which is what a nucleotide weighs inside a chain (dA 313.21, dC 289.18, dG 329.21, dT 304.20 g/mol)
H2O\mathrm{H_2O}
added once, for the terminal hydroxyl groups of the linear molecule
HPO3\mathrm{HPO_3}
removed when the 5′ end is a hydroxyl rather than a phosphate, as in a chemically synthesised oligonucleotide

How it works

Every nucleotide inside a strand is a nucleoside monophosphate that has lost a water in forming the phosphodiester bond. Adding the residue weights of every base, and one water for the two chain ends, gives the molecular weight of a strand that carries a 5′ phosphate. A synthetic oligonucleotide usually has a 5′ hydroxyl and no terminal phosphate, which removes HPO₃ (79.98 g/mol).

For a double-stranded DNA both strands are counted. The second strand is the complement of the one entered. Residue weights are calculated from the IUPAC standard atomic weights, so they agree with the values that vendors print to two decimals.

Worked example

The M13 forward (−20) sequencing primer, GTAAAACGACGGCCAGT, as a single-stranded DNA oligonucleotide with a 5′ hydroxyl.

  1. Composition: 6 A, 4 C, 5 G, 2 T.
  2. Σ = 6 × 313.21 + 4 × 289.18 + 5 × 329.21 + 2 × 304.20 = 5,290.43 g/mol.
  3. MW = 5,290.43 + 18.015 − 79.979 = 5,228.47 g/mol.

The primer weighs 5,228.47 g/mol, so 1 nmol is 5.228 µg and 1 µg is 0.1913 nmol.

These are the values the calculator opens with, so you can check its output against this example.

Assumptions

  • Average (not monoisotopic) molecular weight, for a linear molecule with a 3′ hydroxyl.
  • Natural, unmodified bases. Dyes, biotin, phosphorothioates and other modifications change the weight.
  • The sequence contains only A, C, G and T (or U). Ambiguity codes have no single weight.

Common mistakes

  • Using the 5′ phosphate convention for a synthetic oligonucleotide, which overstates it by about 80 g/mol.
  • Entering both strands of a double-stranded molecule. Enter one strand and choose double-stranded DNA.
  • Treating the weight of a salt form (sodium or ammonium) as the weight of the free acid. The weight here is for the protonated form.

Related tools

DNA and RNA Concentration Calculator (A260)Nucleic acid concentration and purity from absorbanceOpen calculatorGC Content CalculatorGC percentage and base composition of a sequenceOpen calculatorMolecular Weight CalculatorMolar mass and composition from a chemical formulaOpen calculatorReverse Complement ToolReverse, complement or reverse-complement a sequenceOpen calculator

Related equipment

Service documentation, failure modes and parts for the instruments this calculation is used with.