Sodium borate buffer for rapid DNA electrophoresis

Authors

B. J. Stevenson

Summary

A recipe for preparing a 20-times stock solution of sodium borate at pH 8 is given and some information on using this in DNA electrophoresis.

Introduction

Sodium borate is a simple buffer for rapid and cost-effective DNA electrophoresis (Brody & Kern, 2004).

Materials

1. NaOH
2. boric acid
3. deionised water

Hazards:

1. Caustic, can cause severe burns or damage eyes
2. Possible acute or chronic health damage if inhaled or ingested
3. None (in the quanty used here)

Precautions:

Use gloves, safety glasses and lab coat during preparation and use.

Dispose of used buffer by removing any hazardous DNA dyes (e.g. ethidium bromide) with activated carbon, diluting and pouring down a sink.

Procedure

Add 8 g of NaOH pellets and about 48 g of boric acid to 0.9 L of deionised water. Stir until all solids are dissolved.

Adjust the pH to 8 by adding boric acid or NaOH.

Make up to 1 L with deionised water.

Dilute this stock solution 20-fold with deionised water for use in preparing agarose gels and in the gel tank. DNA dye can be added to the gel only, or for uniform results in both the gel and the buffer in the tank.

Anticipated results

Electrophoresis can be run at higher volage compared to Tris-based systems (TAE or TBE). I typically use 10 V/cm for routine analysis or 6 V/cm for high quality results with uniform migration across the gel (no smiling).

Linear DNA will migrate relative to size. Plasmid DNA has unusual migration compared to Tris systems and tend to run slower than expected, especially for supercoild plasmids.

References

Brody, J.R. and S.E. Kern, Sodium boric acid: a Tris-free, cooler conductive medium for DNA electrophoresis. Biotechniques, 2004. 36: p. 214-216.

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