DNA Copy Number Calculator

Plasmid DNA is more stable, can be accurately quantified, and is less prone to contamination of experimental samples. PCR amplicons degrade faster and can easily contaminate reactions (amplicon carryover). However, amplicons are acceptable if handled carefully with strict contamination controls and separate pre/post-PCR areas.

One genome equivalent varies by organism: human = 6.6 pg per diploid cell, E. coli = 4.6 fg per cell, yeast = 12.1 fg per haploid cell, Drosophila = 0.18 pg. These values correspond to approximately 3.0 × 10⁹ copies per µg for a single-copy gene in the human genome, but only ~2 copies per 6.6 pg.

If the mass measurement includes contaminants (RNA, protein, salts), the true DNA mass is less than measured, leading to overestimated copy numbers. Use Qubit (fluorometric, DNA-specific) rather than NanoDrop (A₂₆₀, non-specific) for the most accurate mass input. An A₂₆₀/A₂₈₀ ratio of 1.8-2.0 indicates acceptable purity.

Theoretically, qPCR can detect a single copy, but reliability requires at least 3-10 copies per reaction due to Poisson sampling statistics. At 1-3 copies, stochastic effects cause high variability between replicates. Digital PCR provides more reliable quantification at very low copy numbers by partitioning the sample into thousands of individual reactions.

Copies per µL = Copies per reaction / Volume of template added (µL). If your qPCR uses 2 µL template and detects 5000 copies, the sample contains 2500 copies/µL. For clinical viral loads, this is then multiplied by extraction dilution factors and reported as copies/mL of the original sample.

No. Supercoiling is a conformational property that affects gel migration and some biological activities but does not change the mass or molecular weight of the DNA. The copy number calculation depends only on mass and MW. However, supercoiled DNA may have slightly different fluorometric quantification compared to relaxed or linear forms.

1 femtomole (fmol) = 10⁻¹⁵ mol = 6.022 × 10⁸ molecules (approximately 602 million molecules). This unit is commonly used in next-generation sequencing library preparation. A typical sequencing library load of 20 fmol contains about 1.2 × 10¹⁰ molecules.

The formula is the same, but use 340 Da/nt for ssRNA molecular weight. In practice, RNA copy numbers are measured by first converting to cDNA via reverse transcription, then quantifying by RT-qPCR. For absolute RNA quantification, in vitro transcribed RNA standards with known copy numbers are recommended.

Log₁₀ copy number is used because biological samples span many orders of magnitude (10¹ to 10¹² copies). qPCR standard curves plot Ct (cycle threshold) vs. log₁₀(copies), producing a linear relationship. A perfect standard curve has a slope of -3.32 (corresponding to 100% PCR efficiency) and R² greater than 0.99.