Claude Calculator — Molecular Biology
Small calculators I reach for at the bench. Everything runs locally in your browser — nothing is sent anywhere. Set a molecule once and the mass, mole, and concentration tools all share it.
Molecule
Define what you're working with. Used by the mass↔moles and concentration tools below.
Mass ⇌ Moles
Type in either box — the other updates using the molecular weight above.
Formula: moles = mass / MW · mass = moles × MW
Concentration
Convert between mass and molar concentration. Add a volume to get the total in the tube.
Formula: C(mol/L) = C(g/L) / MW · amount = C × V. Note 1 ng/µL = 1 µg/mL = 1 mg/L.
Dilution — C₁V₁ = C₂V₂
Fill any three boxes; leave the unknown blank. Concentrations cancel, so C₁ and C₂ just need the same unit.
Formula: C₁V₁ = C₂V₂ → e.g. V₁ = C₂V₂ / C₁, diluent = V₂ − V₁.
Leave exactly one box empty to solve for it.
Nucleic acid — A₂₆₀ → concentration
Beer–Lambert at 260 nm. NanoDrop reports a 1 cm-equivalent path, so leave path length at 1 unless you measured otherwise.
Formula: ng/µL = A₂₆₀ × factor × dilution / path (factor: dsDNA 50, ssDNA 33, RNA 40).
Oligos vary a lot — a generic factor is rough. For short oligos use a nearest-neighbour ε (their true ng/µL per A₂₆₀ ranges ~20–35).
Protein — A₂₈₀ → concentration
Either use a known reference protein or compute the extinction coefficient from a sequence (paste one in the Molecule tab, set type = Protein).
Formula: ε₂₈₀ = 5500·nW + 1490·nY (reduced; +125·n(SS) per disulfide if oxidized). A₂₈₀(1 mg/mL) = ε / MW, so conc (mg/mL) = A₂₈₀ × dilution / (path × E₀.₁%).
Purity — what the ratios should be
Typical values for clean samples on a NanoDrop-style spectrophotometer (1 cm equivalent).
| Sample | A₂₆₀/A₂₈₀ | A₂₆₀/A₂₃₀ | Quantify at | Notes |
|---|---|---|---|---|
| Pure dsDNA | ~1.8 | 2.0–2.2 | A₂₆₀ (50 ng/µL) | Below 1.8 → protein or phenol carryover. |
| Pure ssDNA / oligo | ~1.8–1.9 | 2.0–2.2 | A₂₆₀ (33 ng/µL) | Use a sequence-specific ε for short oligos. |
| Pure RNA | ~2.0 | 2.0–2.2 | A₂₆₀ (40 ng/µL) | Below 2.0 → protein/phenol or degradation. |
| Pure protein | ~0.57 | — | A₂₈₀ (ε) | A₂₈₀/A₂₆₀ ≈ 1.75. High A₂₆₀ → nucleic-acid carryover. |
The A₃₂₀ (or A₃₄₀) baseline should sit near zero. A raised tail there means turbidity / particulates / aggregates scattering light — re-blank, re-spin, or filter, and baseline-correct before trusting the ratios.
Purity — what contaminants look like
Diagnosing a bad trace from which ratio is off and where the spectrum bumps.
| Signature | Likely contaminant | Where it comes from |
|---|---|---|
| Low A₂₆₀/A₂₈₀ (DNA <1.8, RNA <2.0); bump ~280 | Protein | Incomplete deproteinization; aromatic residues absorb at 280. |
| Low A₂₆₀/A₂₈₀; shoulder ~270 | Phenol | Phenol/chloroform or TRIzol carryover; phenol peaks ~270 nm. |
| Low A₂₆₀/A₂₃₀ (<~1.8); high A₂₃₀ | Chaotropic / guanidinium salts | Residual GuHCl or GuSCN from spin columns / TRIzol; wash/elution carryover. |
| Low A₂₆₀/A₂₃₀; high A₂₃₀ | EDTA, Tris, other buffer salts | Eluting in TE or carrying over concentrated buffer; absorb near 230. |
| Low A₂₆₀/A₂₃₀ | Carbohydrate / glycogen | Co-precipitated polysaccharide or glycogen carrier. |
| Low A₂₆₀/A₂₃₀; broad ~230 | Residual organics | Ethanol / isopropanol / chloroform not fully evaporated. |
| High A₂₆₀/A₂₈₀ in a protein prep | Nucleic acid | DNA/RNA carryover; correct with Warburg–Christian or nuclease treatment. |
| Raised A₃₂₀/A₃₄₀ baseline; whole trace lifted | Particulates / aggregates / bubbles | Turbidity scatters light across all λ; re-spin, filter, or re-load. |
IUPAC degenerate bases
The full code table, for reference.
| Code | Bases | Meaning | Code | Bases | Meaning |
|---|---|---|---|---|---|
| A | A | Adenine | B | C G T | not A |
| C | C | Cytosine | D | A G T | not C |
| G | G | Guanine | H | A C T | not G |
| T | T | Thymine | V | A C G | not T |
| U | U | Uracil | N | A C G T | any |
| R | A G | purine | W | A T | weak |
| Y | C T | pyrimidine | S | G C | strong |
| K | G T | keto | M | A C | amino |
Bases → code
Enter a set of bases; get the single IUPAC letter that covers exactly them.
Code → bases
Enter one IUPAC letter; get the bases it represents.
Degenerate sequence — expand & reverse-complement
Paste a degenerate sequence (e.g. a primer) to count and enumerate every concrete sequence it encodes, and to get its reverse complement.
Formula: total = Π(degeneracy per position) — single base = 1, R/Y/S/W/K/M = 2, B/D/H/V = 3, N = 4.