DNA Copy Number Calculator

Calculate number of DNA molecules, copy number, and dilutions needed for qPCR standards.

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Where 650 Da Per Base Pair Comes From

The average molecular weight of a double-stranded base pair is about 650 daltons — roughly 330 per nucleotide, doubled. This lets any DNA length be converted to molecular weight, and from there to copy number.

copies/μL = (ng/μL × 10−9 × NA) / (length × 650)
TemplateLengthCopies per ng
Short amplicon200 bp4.6 × 109
Plasmid5 kb1.9 × 108
Human genome (haploid)3.1 Gb~300

The range spans seven orders of magnitude, which is why length must always be specified. A nanogram of short amplicon contains billions of copies; a nanogram of human genomic DNA contains a few hundred.

The 303 figure is worth remembering: 1 ng of human genomic DNA is roughly 300 haploid genome copies, or about 150 diploid cells' worth. Single-cell work and forensic samples operate near this limit.

Why Standard Curves Drift

IssueEffect
Supercoiled plasmidAmplifies less efficiently than linear
Adsorption to plasticSerial dilutions lose material at low concentration
Freeze-thaw cyclesDegradation shifts the curve
A260 overestimatesFree nucleotides and RNA inflate the reading

Linearising plasmid standards before use is standard practice, because supercoiled DNA amplifies with different efficiency and shifts the curve relative to linear targets. Low-bind tubes and carrier nucleic acid reduce adsorption losses at the dilute end.

A260 quantification measures all nucleic acid, including RNA and free nucleotides, so it overestimates the intact target. Fluorometric methods such as PicoGreen or Qubit are dye-based and more specific to double-stranded DNA, which matters when the copy number will define a standard curve.

Worked Examples

Example 1: Plasmid 2000bp at 10ng/μL
MW=2000×650=1.3×10⁶
Result: copies/μL=10e-9×6e23/1.3e6=4.6×10⁹
Standard curve: dilute to 10⁸→10² copies
Example 2: Genomic DNA: human haploid 3×10⁹bp
Genomic copy number from ng amount
Result: 1ng/μL human gDNA ≈ 303 genome copies/μL
Human genome: 3.2×10⁹ bp, MW=2.1×10¹² g/mol
Example 3: Why length dominates
1 ng of 200 bp amplicon versus 1 ng human gDNA
Result: 4.6 × 109 versus about 300 copies
The same mass contains vastly different copy numbers. Length must always accompany a concentration when copy number matters.
Example 4: The single-cell limit
1 ng human genomic DNA
Result: About 300 haploid genomes
Roughly 150 diploid cells. Forensic and single-cell applications operate near this quantity, where stochastic sampling begins to dominate.

Common Mistakes

⚠️
Not specifying template length

Copy number scales inversely with length. A nanogram of 200 bp amplicon contains ten million times more copies than a nanogram of human genomic DNA.

⚠️
Using supercoiled plasmid standards

Supercoiled DNA amplifies less efficiently than linear. Linearise standards so they match the amplification behaviour of the target.

⚠️
Quantifying standards by A260

It measures all nucleic acid including RNA and free nucleotides. Fluorometric methods are more specific to double-stranded DNA.

⚠️
Ignoring adsorption in serial dilutions

DNA binds to plastic, so the most dilute standards lose material. Use low-bind tubes and consider carrier nucleic acid.

Frequently Asked Questions

Why 650 Da per bp?
Average molecular weight per base pair in double-stranded DNA ≈ 650 Da (average of all 4 nucleotides as sodium salts). Use 330 Da for single-stranded DNA or RNA (per nucleotide). Plasmid: circular dsDNA, MW=size×650.
Copy number standards?
Linearize plasmid, calculate copies, make serial dilutions 10⁸→10⁰. Include in qPCR plate. Absolute quantification: compare sample Ct to standard curve. For accurate standards: use ddPCR to verify copy number of your stock solution.
Why 650 daltons per base pair?
It is the average molecular weight of a double-stranded base pair, approximately 330 per nucleotide doubled.
How many copies are in 1 ng of human genomic DNA?
About 300 haploid genome copies, equivalent to roughly 150 diploid cells.
Why linearise plasmid standards?
Supercoiled DNA amplifies with different efficiency than linear template, shifting the standard curve relative to the target being measured.
Why not quantify standards by A260?
Because it detects all nucleic acid including RNA and free nucleotides, overestimating intact target. Fluorometric assays are more specific.