To separate kilobases of DNA (ie plasmids), run a 1% agarose gel. For smaller pieces of DNA a 2% (or higher) gel may be needed. A 1% gel can be run at 3-4 V per cm between the anode and cathode (not per cm of gel). The agarose can be made up in either TBE or TAE buffer - dissolve the correct amount of agarose in buffer using the microwave. You can keep a stock bottle of the solid mixture and melt each time you need to pour a new gel.
Only use ethidium bromide if absolutely necessary. We have stocks of SYBR Safe (dsDNA) and SYBR Gold (ssDNA/RNA).
Adding ethidium bromide: always add ethidium bromide once you have melted your agarose and the sample has cooled a little. Otherwise you end up with vapourised ethidium bromide fumes for the lab to breathe in. Wear gloves at all times, and think about what you touch after the gloves are contaminated. The final concentration of ethidium bromide in your gel should be 0.5 ug/ml (~2ul of our lab stock per gel).
This recipe makes 5x stock.
54g tris
27.5g boric acid
20ml of 0.5M EDTA pH 8.0
make up to 1l with water
This recipe makes a 10x stock.
48.4g tris
11.4 ml acetic acid
7.4g EDTA
Make up to 1l with water (should be approx pH8.5)