PlasmidLab / Free tools / DNA molarity
DNA molarity calculator: ng to pmol
Give a length and either a mass or an amount, and the other one follows. Then set up a ligation: vector length, vector ng and insert length give the insert ng for the molar ratio you want.
Mass and amount
Ligation at a molar ratio
Both pieces are treated as double-stranded here, whichever strandedness is chosen above.
Insert to add
How this is calculated
Molecular weight comes from the length and nothing else. For double-stranded DNA the weight is 617.96 g/mol per base pair plus 36.04; for single-stranded DNA it is 308.97 g/mol per nucleotide plus 18.02. Those are anhydrous molecular weights using the average of the four bases. Each strand is counted with its 5′ phosphate, as restriction fragments have; the +18.02 per strand is the water the two free ends carry. An unphosphorylated oligo weighs about 80 g/mol less, which does not matter at these lengths. A 3,000 bp double-stranded fragment is therefore 3,000 × 617.96 + 36.04 = 1,853,916.04 g/mol, and 100 ng of it is 0.0539 pmol.
Amount is mass over molecular weight: pmol = ng ÷ (g/mol) × 1,000. The ligation works in the other direction. The vector mass gives its amount in pmol, the ratio multiplies that to give the insert amount, and the insert amount times the insert molecular weight gives the insert mass. Length and molar ratio are what matter, so a short insert needs far fewer nanograms than a long one at the same ratio.
Many calculators use the round number 650 g/mol per base pair instead. That shortcut makes a fragment about 5% heavier, so it reports about 5% less material: 100 ng of 3,000 bp comes out as 0.0513 pmol rather than 0.0539 pmol. That is why two calculators disagree on the same numbers. The exact value depends on the real base composition of your sequence, which no length-only formula knows, so treat either number as an estimate good to a few per cent and keep to one calculator within an experiment.
Everything runs in your browser. Nothing you type is sent anywhere.