1. Position the gel tray on an even surface and place the blue gel casting gates in the slots provided.
   
2. Combine agarose powder and running buffer (1 x TAE or 1 x TBE) in an Erlenmayer flask. Melt agarose mixture in a microwave with occasional shaking or place on a heating plate with magnetic stirrer.
   
3. Let the agarose mixture cool down to approx.
   50 - 60 °C (to prevent cracking of the UV-tray as well as leaking).
   
4. For visualisation of bands without a subsequent staining step, incorporate 3 µl ethidium bromide solution (10 mg/ ml) per 100 ml agarose solution (ethidium bromide staining is not recommend in case of subsequent blotting for hybridization to ensure high sensitivity).(Caution: ethidium bromide is a powerful mutagen)
   

5. Pour the agarose solution into the tray; remove air     bubbles with a pipette tip. Insert the required comb(s).

6. Allow the gel to set. The solidification may be completed by rapid cooling at 4 °C.

1. Mix samples 5:1 with loading buffer (e.g. 0.25 % bromphenolblue/ 0.25 % xylene cyanol FF/ 40 % sucrose). Remove combs and casting gates, overlay gel with running buffer (1 x TAE or 1 x TBE), load the samples, close the lid and connect the leads to the power supply.
   
2. Set voltage and current to suit the gel and apparatus. As a guideline for separating unkown samples, run the gel at
   150 V until the bromphenol blue has reached the bottom of the gel (approx. 60 min. with BM 100; 100-150 min. using BM 200 - ethidium bromide containing gels will take longer). As power source, BluePower Plus (200 V/300 mA) is recommended.

RNA Agarose Electrophoresis

For a quick check of a RNA preparation, it is possible to run a DNA gel (see above). For a correct size estimation and when the gel is blotted afterwards, a denaturating gel is neccessary. To prevent degradation of RNA, particular caution needs to be applied: always wear gloves; use DEPC-treated buffers (MOPS contains amines and therefore DEPC-treated, already autoclaved H₂0 has to be used). Electrophoresis units, trays, combs, etc. should be soaked overnight in DEPC-treated, autoclaved water. Never use electrophoresis units that are used to check plasmid preparations (they are highly contami-nated with RNases!).

1. Position the gel tray on an even surface in a fume hood and place the blue gel casting gates in the slots provided.
   
2. For a 150 ml 1% denaturing gel combine 1.5 g agarose powder 109.5 ml H₂0 and 15 ml 10 x MOPS (0.2 M MOPS; pH 7.0/ 0.08 M NaAc/ 0.01 M EDTA) in an Erlenmayer flask and melt.
   
3. Let the agarose cool down to approx. 50 - 60 °C.
   
4. In a fume hood add 25.5 ml 37% formaldehyde (should the formaldehyde contain solid paraformaldehyde particles, open a new bottle or at least filter the solution to remove the paraformaldehyde) and immediately pour the agarose solution into the tray. Remove air bubbles with a pipette tip. Insert the required comb.
   
5. Allow the gel to set (30 - 60 minutes at room temperature).