DNA Copy Number and Molarity Calculator

Background.

This calculator converts a mass concentration of double-stranded DNA into the three things people actually need downstream: how many molecules are present, what molar concentration that represents in nanomolar, and how many femtomoles sit in a given volume. It also runs the calculation backwards — tell it how many copies your next step needs and it returns the mass and the pipetting volume that deliver them.

The arithmetic is short. Divide the mass by the molar mass of one molecule to get moles, then multiply by Avogadro's number to get molecules. The molar mass of one molecule is its length in base pairs multiplied by the average mass of a base pair. Everything therefore rests on a single constant, and that constant is where calculators quietly disagree with each other.

Protocol books commonly use 650 grams per mole per base pair. Other sources use 660. Neither is a measurement so much as a convenient round figure. This page instead derives the base-pair mass from values measured and published by NIST: Duewer and colleagues tabulate the A·T base pair at 659.347 g/mol and the G·C base pair at 660.336 g/mol in the sodium salt form, and 617.400 and 618.388 respectively as the free acid, with stated uncertainties and IUPAC standard atomic weights behind them. The page interpolates between the two according to the GC content you enter, and shows the resulting base-pair mass as an output so the number driving your answer is never hidden. The consequence worth knowing up front is that this calculator returns copy numbers about 1.5 percent lower than one using 650, and about 6.8 percent lower again if you switch salt form — so if you are reconciling two tools, check the constant before you check the arithmetic.

The salt form is a genuine choice rather than a display option. Sodium salt and free acid differ by roughly 42 grams per mole per base pair, which is 6.4 percent, and that difference propagates straight into the copy number. Which one is right depends on how your DNA was prepared and what your downstream calculation assumes, so both are offered by name rather than one being chosen for you.

The most important caveat is not arithmetic at all, and it belongs here rather than in an FAQ. Converting mass into molecules assumes that every molecule in the tube is intact and exactly the length you entered. Real preparations are not like that: nicked, sheared and partially degraded DNA carries mass and contributes to your absorbance or fluorescence reading, but does not amplify as a full-length template. A mass-derived copy number is therefore an upper bound on the amplifiable copies present, and the gap widens with every freeze-thaw cycle. This is exactly why NIST assigns certified values to its human genomic DNA standard using PCR-based copy-number methods rather than deriving them from mass. Use this page to prepare a standard curve, to hit a molar ratio for cloning, or to sanity-check an order of magnitude. Do not use it to report an absolute copy number where the answer matters.

Finally the scope: double-stranded DNA only. A single strand's average residue mass depends on that strand's own G-to-C split, not merely on the duplex GC fraction, so halving a base-pair mass would be an unstated approximation. If you have an oligonucleotide, compute its exact molecular weight from the sequence instead — our primer GC content calculator does that, and an exact mass always beats an average.

What is dna copy number & molarity calculator?

Copy number is simply the count of individual DNA molecules in a sample, and it is obtained from a mass concentration by way of the mole. One mole of anything contains exactly 6.02214076 × 10²³ entities — an exact value since the 2019 redefinition of the SI, not a measured one — so the number of molecules in a sample is its mass in grams divided by its molar mass in grams per mole, multiplied by Avogadro's number. For a polymer like DNA the molar mass is not looked up; it is built from the length. A double-stranded molecule of L base pairs has a molar mass of L multiplied by the average mass of one base pair, which depends on base composition because an A·T pair and a G·C pair have slightly different masses, and on salt form because DNA is normally handled as its sodium salt rather than as the free acid. Molarity is the same information in different clothing. Because 1 nanomolar is exactly 1 femtomole per microlitre — both reduce to 10⁻¹⁵ moles per microlitre — the molar concentration and the copy number differ only by Avogadro's constant, which is why a page that reports one should report the other rather than sending you to a second calculator. Molar units are what cloning protocols speak: Gibson assembly and ligation reactions specify insert-to-vector ratios in moles because what matters is how many ends are available to join, not how many nanograms are present. Copy number is what quantitative PCR speaks, because a standard curve is a dilution series of known molecule counts. The same three inputs answer both questions.

How to use this calculator.

1. 01Enter the DNA concentration in ng/µL. This is the same number as µg/mL. If you have only an absorbance reading, convert it first with our DNA concentration calculator.
2. 02Enter the length of one molecule in base pairs — the entire plasmid including the insert, the full amplicon length including primer sequences, or the genome size. Copy number scales as one over this figure, so an error here scales the answer proportionally.
3. 03Enter the volume you care about to get total copies and total femtomoles for that reaction or aliquot.
4. 04Set the GC content of your fragment. It matters far less here than it does for melting temperature — the whole 0 to 100 percent span moves the answer by only 0.15 percent — but it is exposed rather than assumed because the base-pair mass genuinely depends on it.
5. 05Choose the salt form. Sodium salt is the default and the usual assumption. Switching to free acid raises the copy number by about 6.8 percent, so match whichever form your downstream protocol or your comparison calculator assumes.
6. 06Read the base-pair mass output. If your answer disagrees with another tool, that number is almost always why — many calculators hard-code 650 g/mol and do not show it.
7. 07Enter a target copy number to get the mass and the pipetting volume that deliver it. For a qPCR standard curve, use the top point of your dilution series here.
8. 08Treat the result as an upper bound on amplifiable template, not as a measurement of it.

The formula.

Six lines run the whole page, and only the first carries any judgement.

m_bp = (1 − f_GC) × m_AT + f_GC × m_GC M = L × m_bp n/µL = (c × 10⁻⁹) / M copies/µL = n/µL × N_A nM = n/µL × 10¹⁵ mass for a target = (target / N_A) × M × 10⁹ [ng]

The first line interpolates a base-pair mass between the measured A·T and G·C values at the GC fraction you supply. The second scales it by length. The third converts nanograms per microlitre to grams per microlitre by multiplying by 10⁻⁹, then divides by grams per mole to leave moles per microlitre. The fourth multiplies by Avogadro's constant, which is exact, so it introduces no error of its own.

The fifth line deserves a note because the exponent looks arbitrary and is not. Moles per microlitre becomes moles per litre by multiplying by 10⁶, and moles per litre becomes nanomolar by multiplying by 10⁹, so the combined factor is 10¹⁵. That same 10¹⁵ converts moles per microlitre to femtomoles per microlitre — which is the arithmetic behind the identity 1 nM ≡ 1 fmol/µL. This page reports femtomoles in the whole volume rather than per microlitre, so that the two outputs carry genuinely different numbers rather than printing the same value twice.

The last line is the inverse. It is worth noting that the mass containing a target copy number does not depend on your sample's concentration at all — it is a property of the molecule. Only the pipetting volume depends on how concentrated your sample happens to be.

Rounding stage: FINAL ONLY. The base-pair mass, the duplex molar mass and the moles per microlitre are all carried at full precision — forty significant digits internally, because the chain spans about thirty orders of magnitude between 10⁻⁹ grams and 10²³ molecules — and rounding to ten decimal places happens once, per field, at the return. Rounding the base-pair mass to 660 before multiplying by 5000 base pairs would move the duplex mass by nearly 800 g/mol and shift the copy number in its fourth significant figure.

Invalid-domain behaviour. A fragment length of zero or less is rejected, because it gives a molar mass of zero and makes the moles calculation singular. A GC content outside 0 to 100 percent is rejected, because no such composition exists. Negative concentrations, volumes and target copy numbers are rejected. A concentration of exactly zero is accepted: copies, molarity and femtomoles are all zero, and the volume needed to deliver a target is unbounded, so it returns zero with the note saying so rather than an infinity.

A worked example.

Frequently asked questions.

References& sources.

1. [1]Duewer, D. L., Kline, M. C., Romsos, E. L. & Toman, B. (2018). 'Evaluating droplet digital PCR for the quantification of human genomic DNA: converting copies per nanoliter to nanograms nuclear DNA per microliter.' Analytical and Bioanalytical Chemistry. PRIMARY SOURCE — NIST authors, open access, underpinning SRM 2372a. Supplies every base-pair mass used here: A·T 659.347(2) and G·C 660.336(2) g/mol in the sodium salt form, A·T 617.400(2) and G·C 618.388(2) g/mol as the free acid, and a weighted mean of (659.743 ± 0.003) g/mol for genomic DNA at 60:40 AT:GC — a figure this calculator reproduces exactly when GC content is set to 40 percent. The paper states its atomic masses come from Meija et al. (2016), the IUPAC standard atomic weights. Fetched and every value verified 2026-07-29.
2. [2]National Institute of Standards and Technology / CODATA, 'Avogadro constant' — fundamental physical constants database, CODATA revision 2022. STANDARDS BODY. Gives N_A = 6.022 140 76 × 10²³ mol⁻¹ with no uncertainty, because the value has been exact since the 2019 redefinition of the SI base units. Retrieved and verified 2026-07-29.
3. [3]National Institute of Standards and Technology, Standard Reference Material 2372a, 'Human DNA Quantitation Standard' — certificate of analysis. STANDARDS BODY, cited for scope rather than for a constant. NIST assigns certified values of DNA mass concentration and copy number to this material using PCR-based methods rather than deriving copy number from mass, which is the clearest available statement that a mass-derived copy number and an amplifiable copy number are different quantities. Retrieved 2026-07-29.
4. [4]Commission on Isotopic Abundances and Atomic Weights (CIAAW), IUPAC — Standard Atomic Weights 2021. STANDARDS BODY, upstream provenance. The base-pair masses cited above are themselves built on IUPAC standard atomic weights, and this table is the authority for those values and for the interval form in which several of them are published — which is why the base-pair masses carry uncertainties in their final digit rather than being exact. Table page fetched 2026-07-29.