1.  GEL PREPARATION
For gel preparation, dilute the Super Agarose 10% suspension to a required agarose concentration with an electrophoretic buffer. To prepare 50 ml of 1% gel, pour 45 ml of an electrophoresis buffer into a glass flask and pipet 5 ml of the suspension into the buffer. Use repeated pipetting of the electrophoretic buffer to wash the residual agarose from the pipette. Mix the diluted suspension and heat it to boiling in a microwave or on a hot plate with stirring, until all the agarose is melted and dissolved to form a clear homogenous solution. Cool the solution to 60 - 70 C and add dye if desired. Pour the molten Super Agarose into an electrophoretic tray, position the comb in the molten gel and allow it to harden by storing at room temperature for 1 - 1.5 hr.

2.  SAMPLE LOADING
Gently remove the comb from the hardened Super Agarose gel. Mix DNA or RNA samples with a glycerol-dye loading solution and load them into the application slots with the gel placed in the electrophoretic apparatus and submerged in the buffer. Alternatively, first load samples into the application slots and then place the tray with gel into the electrophoresis apparatus filled with buffer. For RNA denaturing gels, perform denaturation with either formaldehyde or glyoxal and load the denatured RNA samples into the application slots.

3.  ELECTROPORESIS
Perform electrophoretic separation of nucleic acids according to your standard protocol. With a 1 - 1.5% gel, optimal separation is achieved by applying 5 - 7 V per cm of gel length. Under these conditions, 0.2 - 20 kb DNA fragments separate in 0.5 - 1.5 hours using a mini=gel (up to 10 cm long) and in 2 - 4 hours using a long gel (15 - 20 cm long). RNA separates in 1 - 2 or 2 - 4 hours using a mini-gel or long gel apparatus, respectively.

1. Different applications call for varying agarose concentrations. For electrophoretic separation of RNA in northern blotting, either in formaldehyde or glyoxal gels, the recommended agarose concentration is usually 1%. For Southern blotting, the typical agarose concentration is 0.8 - 1.2%. Separation of PCR products 0.1 - 2kb long requires electrophoresis in a 1.5 - 3.5% gel.
   
2. When working with multiple samples, load samples into the application slots and start electrophoresis as quickly as possible. Delays during sample application permit premature diffusion of RNA and DNA molecules into the gel. This frequently results in a "railroad track" appearance of DNA or RNA bands, caused by accumulation of molecules at the left and right edges of the application slot. To accelerate uniform entrance of DNA and RNA into the gel, run the gel at 100 V for the first 2 - 3 minutes of electrophoresis.