Southern blot depurination solution (0.25 M HCl) recipe
A weak acid that partially nicks DNA in the gel so large fragments (>10 kb) transfer efficiently.
🧮 Volume calculator
| Component | Amount | Final concentration (1X) |
|---|---|---|
| Concentrated HCl (37%, ≈12.1 M) | 10.35 mL | 0.25 M |
| Water (distilled) | to final volume |
Steps
- Add the concentrated HCl to water (acid into water).
- Soak the gel for 10–15 min with shaking (bromophenol blue turns yellow).
- Rinse with water and move on to denaturation.
Good to know
- Over-treatment fragments DNA too much and weakens the signal.
⚠ Safety HCl is corrosive — wear gloves and goggles.
FAQ
Is it needed for small fragments?
It can be skipped if all fragments of interest are under ~5 kb.
This is a widely used standard composition. Amounts depend on the hydrate form and purity of your reagents — check the formula weight (FW) on the bottle and follow your institution's safety rules and the manufacturers' instructions.