Preparation of Agarose Gels for DNA separations

Weigh out the desired amount of agarose and place in an Erlenmeyer flask with a measured amount of electrophoresis buffer, e.g. for an 0.8% gel, add 0.8 gm of agarose and 100ml of TBE Buffer (1X), to a 200 ml flask. The larger flask insures against the agarose boiling over. Dissolve the agarose in a boiling water bath or in a revolving-plate microwave oven. All the grains of agarose should be dissolved and the solution clear. Cool the solution to 60°C (70°C for concentrations 2% or above) and pour immediately. Allow the gel to set for one-half hour before using. Make sure to use the same electrophoresis buffer in the gel as for the running buffer.

DNA Size Separation by Agarose Concentration
 

Prepare sample by adding concentrated DNA loading buffer. DNA always migrates towards the positive electrode. Bromophenol blue (BP) generally co-migrates with 0.5 kb fragments of DNA. Stain with 0.5 mg/ml ethidium bromide for 10 minutes.