DNA Molarity Calculator: nM and pmol of Double-Stranded DNA

This calculator converts a double-stranded DNA concentration in ng/µL into a molar concentration in nM, and gives the picomoles in a volume. Enter the concentration, the volume in µL and the length of the DNA in base pairs (bp); you also get the molecular weight used.

Formula

MW = bp × 617.96 + 36.04 g/mol; nM = c × 10⁶ ÷ MW; pmol = c × V × 1000 ÷ MW.

• MW: 617.96 g/mol per base pair, the average for double-stranded DNA in the anhydrous free-acid form, plus 36.04 g/mol for the ends; the often quoted 650 or 660 g/mol per base pair is for the sodium salt, so results differ by about 6% depending on the convention
• c: concentration in ng/µL (equal to mg/L)
• V: volume in µL; c × V is the mass in ng
• ng ÷ (g/mol) gives nmol, and 1 nmol = 1000 pmol

Worked Example

A 3,000 bp double-stranded DNA at 50 ng/µL; 10 µL of it.

1. MW = 3000 × 617.96 + 36.04 = 1,853,916.04 g/mol
2. Concentration: 50 × 1,000,000 ÷ 1,853,916.04 = 26.97 nM
3. Mass in 10 µL: 50 × 10 = 500 ng; amount: 500 × 1000 ÷ 1,853,916.04 = 0.2697 pmol

Assumptions

• The DNA is double-stranded and linear or circular; for single-stranded DNA or RNA use a different weight per nucleotide.
• The average weight per base pair is used, so the result does not depend on the exact sequence; the error is usually well under 1%.
• The concentration reading is correct and the sample is free of RNA and other contaminants.

How to read the result

A molar concentration is what reaction set-ups usually ask for, because they compare numbers of molecules, not masses. Longer DNA of the same mass has fewer molecules: 50 ng/µL of a 3,000 bp fragment is about 27 nM, while the same mass concentration of a 300 bp fragment is about ten times more. For a ligation set-up, use the ligation calculator.

Limits and common mistakes

• Entering the length in kb instead of bp gives a result 1000 times too large.
• Using the double-stranded weight for single-stranded DNA roughly halves the molarity.
• Mixing pmol and nM: nM is pmol per mL, and pmol per µL is µM.

Frequently Asked Questions

How do I convert ng/µL of DNA to nM?

Multiply by 10^6 and divide by the molecular weight, bp × 617.96 + 36.04 g/mol.

What is the molarity of a 3,000 bp DNA at 50 ng/µL?

About 26.97 nM.

What molecular weight does one base pair have?

About 618 g/mol (617.96) for double-stranded DNA in the anhydrous free-acid form; the 650 or 660 g/mol often quoted is for the sodium salt, so results differ by about 6% between the two conventions.

How many pmol are in 500 ng of a 3 kb fragment?

About 0.2697 pmol.

in c | DNA concentration | ng/µL | 50 | 0
in v | Volume | µL | 10 | 0
in bp | Length | bp | 3000 | 1
out nm | Molar concentration | nM | c * 1000000 / (bp * 617.96 + 36.04) | 2
out pmol | Amount in the volume | pmol | c * v * 1000 / (bp * 617.96 + 36.04) | 4
out mw | Molecular weight of the dsDNA | g/mol | bp * 617.96 + 36.04 | 2