Essential biochemistry calculations — molecular weight, mass-to-moles conversion, A260 concentration determination, C1V1 dilution, copy number, protein extinction coefficient, buffer preparation recipes, and unit conversion. Also: Sequence Analysis | Genetics Calculator.
Enter a DNA/RNA sequence, protein sequence (single-letter code), or chemical formula to compute molecular weight.
Enter molecular weight and mass to calculate moles, or moles to calculate mass needed for a target volume and concentration.
Enter A260 reading to calculate nucleic acid concentration. Optionally enter A280 for purity ratio (A260/A280).
Use the C₁V₁ = C₂V₂ formula to calculate dilutions. Enter stock concentration, target concentration, and target volume.
Enter template length and mass to calculate the number of DNA/RNA copies.
Enter a protein sequence to calculate extinction coefficient at 280 nm using the Edelhoch method (Trp, Tyr, Cys contributions).
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Select a buffer and enter target volume to get the preparation recipe.
Select a category and units to perform common biochemistry unit conversions.
References: A260 conversion factors: dsDNA=50 µg/mL, ssDNA=33 µg/mL, RNA=40 µg/mL per 1.0 OD. Average nucleotide MW: ~330 Da (dsDNA). Protein extinction at 280 nm: Trp=5690, Tyr=1280, Cys(Cystine)=120 M⁻¹cm⁻¹. Buffer recipes based on standard molecular biology protocols (Sambrook & Russell).
What is a mole — and why does it run every panel on this page?
Molecular biology keeps asking one question in different costumes: how many molecules do I actually have? A balance reads grams, a spectrophotometer reads absorbance, a pipette measures microlitres — but reactions count moles, the chemist's unit of 6.022×10²³ molecules per mole. Molecular weight (in daltons, numerically the same as g/mol) is the exchange rate between what you can weigh and what you can count. Every panel above — MW, Mass↔Moles, OD260, Dilution, Copy Number, Extinction Coefficient — is one step on that exchange.
The one number to remember: 1 µg of 1000 bp double-stranded DNA holds about 9.1×10¹¹ molecules. Not a typo — the amounts you pipette are astronomically large on the molecular scale, which is why converting between mass, concentration and copy number matters so much.
Mass, moles and molarity
The Mass↔Moles panel divides grams by g/mol to get moles, and divides moles by litres to get molarity. Worked example: 1 mg of a 50 kDa protein is 1×10−3 g ÷ 50,000 g/mol = 2×10−8 mol = 20 nmol; dissolved in 1 mL, that is a 20 µM solution. Genomic DNA is often discussed in micrograms, oligos and plasmid preps in pmol, and the Unit Conv panel shuttles between all of these prefixes.
OD260: concentration without weighing
Nucleic acids absorb UV at 260 nm following the Beer–Lambert law (absorbance = extinction × concentration × path length), so a spectrophotometer can replace a balance. For a 1 cm path, one absorbance unit corresponds to roughly 50 µg/mL of double-stranded DNA, 40 µg/mL of RNA, or 33 µg/mL of single-stranded DNA. The optional A280 reading gives a purity heuristic: clean DNA sits near an A260/A280 ratio of 1.8 and clean RNA near 2.0; a low ratio usually means protein or phenol tagging along. A ratio well above 1.8 in a DNA prep points the other way: RNA tagging along.
Dilution: C₁V₁ = C₂V₂
The dilution formula is just conservation of solute: the moles you draw from the stock equal the moles you deliver. To go from a 100 mg/mL stock to 10 mg/mL in a final volume of 100 mL: V₁ = (10 × 100) / 100 = 10 mL of stock plus 90 mL of solvent, a 10-fold dilution. The Buffer Prep panel runs the same arithmetic with “50×” or “10×” stock factors — making 1 L of 1× TAE from a 50× stock takes 1000/50 = 20 mL of stock.
Copy number and extinction coefficients
Because every copy of a plasmid has the same molecular weight (about 660 Da per base pair for dsDNA), mass converts to molecule count through Avogadro's number: 1 µg of a 5000 bp plasmid is roughly 1.8×10¹¹ copies, and 1 pmol of anything is 6.02×10¹¹ copies. For proteins, the Edelhoch method predicts absorbance at 280 nm from just three residue types: each tryptophan contributes 5690 M⁻¹cm⁻¹, each tyrosine 1280, each cystine (disulfide) 120. A protein with no aromatic residues is nearly invisible to UV — weigh it instead.
Common misunderstandings
“An OD of 1 is an exact constant.” The 50/40/33 µg/mL factors are empirical averages for long polymers; base composition, salt and especially short oligonucleotides shift them.
“660 Da per base pair is a law of nature.” It is a convenient average — AT- and GC-rich DNA differ slightly, and salt conditions matter. Do not trust more than two significant figures.
“An A260/A280 of 1.6 ruins my sample.” The ratio is a screening heuristic, sensitive to pH and buffer; treat it as a flag, not a verdict.
“Copies and pmol are interchangeable.” They differ by a factor of 6.02×10¹¹; mixing them up is a classic qPCR setup error.
