CH 6 · notes
Assumptions
DNA copy number calculator for one double-stranded molecule: enter the length in base pairs and either a mass in nanograms, a copy count, or an amount in picomoles. The page returns the other amounts. Leave the volume blank and it does not invent a concentration.
Double-stranded DNA only. One base pair is 650 grams per mole, with no end correction. That is the average written in the NEB PCR cloning ligation protocol, and it is the same convention the ligation page uses for mass and moles. A calculator that adds an end correction, or that uses about 660 or about 618 grams per mole, will not match these picomoles or these copies, especially on a short fragment. Single-stranded DNA and RNA have a different mass per residue, so they are not accepted here.
The Avogadro constant is the exact SI defining value, 6.02214076×10^23 per mole. Copies are picomoles times that constant, divided by 1×10^12, because one picomole is 10^−12 mole. The page checks that this route agrees with mass times the same constant divided by length, 650, and 10^9. If the two routes ever disagreed, it would not show a number.
The default conversion is nanograms to copies. The other three choices are copies to nanograms, nanograms to picomoles, and picomoles to nanograms. Switching the choice before you type does not invent a mass or a copy count. Fields start empty.
How it works
pmol = ng × 1000 ÷ (bp × 650)
copies = pmol × 6.02214076e+23 ÷ 1e12
650 g/mol per bp, dsDNA, no end correction
Picomoles come only from the shared dsDNA module: nanograms times 1000, divided by length times 650. Nanograms from picomoles are that relation run backwards. Femtomoles are picomoles times 1000. None of those three lines is rewritten on this page.
Display is four significant figures, half away from zero, the same window as the solution channels. A value whose order of magnitude sits outside that window is scientific notation. On the LCD, the working lines, and the prep steps that form is a power of ten, such as 3.088 × 10⁸, and a negative power uses a superscript minus. Copy result and Copy protocol keep the e notation, such as 3.088e+8, so a spreadsheet can read the same characters. A modest count that still fits the window stays in fixed point. The working lines do not round the constant down to 6.022×10^23, and they do not round copies to a nearby whole number.
An optional volume is converted with the shared volume scale, litres, millilitres, and microlitres. Copies per microlitre are the copy count divided by that volume after it is in microlitres. One millilitre is exactly 1000 microlitres. The page does not store its own threshold and it does not warn about pipette size. Prep steps quote the same strings: the mass or the copies you typed, the calculated amounts, and, only when a volume is filled in, the concentration in that volume. They do not name a dilution buffer, a genome, or a sequencing depth.
Copy result is only the headline display: the copy count when you convert from mass, the picomoles when that is the chosen result, or the nanograms when mass is the unknown. Copy protocol is the longer text, including the mode, the length, every amount, the volume when you entered one, the numbered steps, and the working lines. Print uses the site print stylesheet. The footer under the steps is molicheck.com/dna-copy-number.
Length is a positive whole number of base pairs. A decimal, zero, or a negative length returns no result. Mass, copies, picomoles, and volume accept a positive number in scientific notation, such as 1e6 copies. The exponent magnitude stops at 99. A larger exponent, a blank field, zero, or a negative number returns no result. An empty volume is omitted. A volume of zero is rejected, so it cannot be read as “no volume”.
Worked example
Length 3000 bp, mass 1 ng, volume 10 µL. The copy number is 3.088 × 10⁸ copies. The amount is 0.0005128 pmol (0.5128 fmol). The mass is 1.000 ng. In that volume, the concentration is 3.088 × 10⁷ copies/µL.
- pmol = 1 ng × 1000 ÷ (3000 bp × 650 g/mol) = 0.0005128 pmol
- fmol = 0.5128 fmol
- copies = 1 ng × 6.02214076 × 10²³ ÷ (3000 bp × 650 g/mol × 1e9) = 3.088 × 10⁸ copies
- copies/µL = copies ÷ 10 µL = 3.088 × 10⁷ copies/µL
- Start with 1 ng of 3000 bp dsDNA.
- That is 0.0005128 pmol (0.5128 fmol) and 3.088 × 10⁸ copies.
- In 10 µL, the concentration is 3.088 × 10⁷ copies/µL.
Common mistakes
Treating the rounded copy count as exact input. The screen figure 3.088 × 10⁸ is four significant figures of a longer fraction. Typing that rounded count back in will not return exactly one nanogram. The forward calculation from one nanogram is the one this example locks.
Using a single-stranded molecular weight, or adding the mass of the terminal phosphates, and then expecting the same picomoles. This page will not match that result. The formula card states the convention in the same words as the ligation page: 650 g/mol per base pair, double-stranded DNA, no end correction.
Forgetting the 10^12 between picomoles and moles. Multiplying picomoles by Avogadro’s number alone counts 10^12 too many copies. The working line writes the division.
Leaving the volume at zero. Zero is invalid. Blank means you do not want copies per microlitre. A volume in millilitres is converted; it is not treated as if it were already microlitres.
FAQ
Is this double-stranded DNA only?
Yes. Amounts use 650 g/mol per base pair of double-stranded DNA, with no end correction. Single-stranded DNA and RNA are not accepted.
Which Avogadro constant is this?
The exact SI defining constant, 6.02214076e+23 per mole. Picomoles convert to copies by multiplying by that constant and dividing by 1e12.
Do I have to enter a volume?
No. Leave it blank and the page still gives copies, nanograms, and picomoles. A filled volume adds copies per microlitre. Zero is not the same as blank.
Why is a large copy number written with an e?
Display is four significant figures, the same rule as the other calculators. Numbers outside that fixed window, including the plasmid example, use scientific notation.
Sources
- NEB. Ligation protocol for the PCR cloning kit (E1202). States 650 daltons per base pair. This page uses that figure as 650 g/mol per base pair of double-stranded DNA, with no end correction.
- BIPM. SI defining constants. The Avogadro constant is defined as exactly 6.02214076×10^23 per mole. This page uses that exact value, not a rounded 6.022×10^23.
Open the home index for the other calculators. Ligation uses the same 650 g/mol line and does not count copies. Primer Tm is a melting temperature.