Second or third year undergraduate

Molecular biology practical

Master mixes, gels, and nucleic acid quantitation, plus the primer and assembly maths that students most often get wrong on their first attempt.

12 calculators, in the order the course uses them. Every one shows its working, flags the hazards, and keeps working offline once the page has loaded. Free, and no account is needed.

Start with Simple dilution All topics and reference tables

In course order

What this practical calculates

1. Simple dilution

C₁V₁ = C₂V₂, exactly how much stock and diluent to mix.

How it works · Practice problems · C₁ · V₁ = C₂ · V₂

2. PCR master mix

Scale a per-reaction recipe to a batch, with overage.

How it works · mix = per-reaction x samples x (1 + overage)

3. Agarose gel

Grams of agarose for a % gel and casting volume.

How it works · Practice problems · agarose (g) = % / 100 · V (mL)

4. Nucleic acid (A260)

DNA and RNA concentration and purity from absorbance.

How it works · Practice problems · c = A260 x factor x dilution

5. DNA: ng to pmol

Convert a dsDNA mass to moles (and back) from its length.

How it works · Practice problems · pmol = ng x 1000 / (660 x bp)

6. Oligo resuspension

Resuspend a lyophilized primer to a stock concentration.

How it works · Practice problems · V = nmol / C

7. Oligo melting temperature (Tm)

Nearest-neighbor Tm with Na+ and Mg2+ salt corrections. Not a Wallace guess.

How it works · Practice problems · Tm = ΔH / (ΔS + R·ln(C_T/x)), salt-corrected

8. Ligation ratio

Insert mass for a target insert:vector molar ratio.

How it works · Practice problems · ng insert = ratio x ng vector x (insert bp / vector bp)

9. Gibson / ligation planner

Vector amount and insert ratios to an exact pipetting table.

How it works · V = (vector_pmol · ratio) / (stock_ng/µL · pmol_per_ng)

10. qPCR fold change (ddCt)

Livak 2^-ddCt with proper error propagation and an honest asymmetric band.

How it works · Practice problems · fold = 2^(−ΔΔCt); band = 2^(−(ΔΔCt ± SD))

11. Transformation efficiency

Colonies, plated fraction, and DNA mass to CFU per µg.

How it works · Practice problems · CFU/µg = colonies · (total / plated) / (ng / 1000)

12. Nucleic acid copy number

Mass, molarity, and copies/µL for dsDNA, ssDNA, or ssRNA, both directions.

How it works · Practice problems · copies/µL = (ng/µL · 1e-9 / MW) · N_A

Worth telling students once

The mistakes this practical produces every year

The 4xGC + 2xAT rule of thumb for primer Tm is only reasonable below about 14 bases. The Tm calculator uses nearest-neighbour thermodynamics and states the salt conditions it assumes.

The OD factor for A260 differs by nucleic acid type: 50 for double-stranded DNA, 40 for RNA, 33 for single-stranded. Using 50 for everything overstates the concentration.

For the person running the course

If you want this page named for your course

What it costs

Nothing, for you and for your students, permanently. There is no licence to sign, no account for students to create, no data to hand over, and nothing for your IT department to approve or install.

What you would get

A page named for your course, with your calculations in your order and your conventions, at a stable URL you can paste into your course management system once and reuse every year.

What we would like back

To be told when it is wrong. If a value, a convention, or a hazard note does not match how your course teaches it, that is a bug worth fixing.

Ask for a page for your course

The honest caveat

Aliquot is an educational aid, not a safety authority and not a certified instrument. Students should verify critical values and follow the safety data sheet and your institution's protocols.

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