Bench Calculators
Solve a dilution for its one missing quantity, and scale a vendor's reaction setup into a master mix.
| Reached by | Tools → Bench Calculators |
| Sample project | Primer test |
What it does
Two pieces of arithmetic that come before almost every experiment, in one panel with two tabs.
Dilution. Fill three of stock concentration, stock volume, final concentration and final volume, each in whatever unit you work in, and the fourth is calculated in the unit you chose for it. The answer comes with the fold dilution and the volume of diluent to add to the stock.
Master mix. Pick a polymerase's published reaction setup, the reaction volume and the number of reactions. Every component is scaled with the vendor's final concentrations kept, water makes up the volume, and the template is added to each tube rather than to the mix. Add overage for pipetting loss, or replace the vendor setup with your own recipe.
What this computes
- Solved quantity: C₁V₁ = C₂V₂ for the one quantity left empty, from molar (M to fM), mass per volume (mg/mL to ng/mL), fold (X) or percent concentrations, and volumes from litres to nanolitres.
- Fold dilution: C₁/C₂.
- Diluent volume: V₂ − V₁, in the final volume's unit.
- Scaled reaction setup: each component's volume per reaction at the chosen reaction volume, in proportion to the vendor's published columns, with the vendor's final concentration beside it.
- Water to volume: the reaction volume less every other component.
- Master mix volumes: each shared component × reactions × (1 + overage).
- Dispense per tube and mix to prepare.
When you'd use this
- Diluting a 100 µM primer stock to a 10 µM working stock, or a plasmid prep to a loading concentration.
- Setting up a plate of PCRs without writing the recipe out by hand.
- Scaling NEB's 20 µl or 50 µl Phusion setup to a 25 µl reaction.
Controls
| Control | What it does |
|---|---|
| C₁, V₁, C₂, V₂ and their units | Leave exactly one empty; it is solved. |
| Reaction setup | The vendor setup to scale. |
| Reaction volume | Volume of one reaction. |
| Template volume | Template per reaction, added to each tube (the vendor leaves it to you). |
| Include DMSO | Adds the setup's optional DMSO (3% final for Phusion). |
| Reactions, overage | How many reactions the mix is for, plus extra as a percent of the mix. |
| Components | Your own recipe instead of a vendor setup. |
Limitations
- A dilution can only lower a concentration; asking for a higher one is refused rather than answered with a negative volume.
- Molar and mass concentrations cannot be mixed in one dilution: converting between them needs the molecule's molar mass.
- Volumes are assumed to add on mixing.
- Only NEB's Phusion setup is bundled today. A custom recipe is not checked against any polymerase's requirements.
Provenance
The Phusion setup is NEB's own published protocol for M0530, cross-checked against the copy NEB published on protocols.io. Its 20 µl and 50 µl columns both come out of the same scaling.
Melting Temperature
Compute the melting temperature of an oligo under conditions you state, rather than under conditions a tool assumed.
Codon Optimization
Rewrite a coding sequence for expression in a chosen host while holding the constraints that matter: forbidden restriction sites, GC window, homopolymer limits, and the encoded protein.