Polyacrylamide Gel Electrophoresis of Oligonucleotides

1. Pour and polymerize a 20% polyacrylamide gel, no Urea.

2. Remove clamps. Rinse with water. Remove comb. Rinse top of gel well.

3. Insert comb teeth down until teeth just touch the gel. Mount the plates in apparatus. Fill chambers with 0.5X TBE and prerun at low wattage for 10 min.

4. Load oligonucleotides to gel.

5. Run narrow gels at 35 W. Run wide gels at 80 W. Run until Bromophenol Blue is 3/4 way down.

6. Decant buffer from apparatus. Remove gel and lay flat.

7. Remove comb and side spacers. Pry apart plates with a spatula. If the gel is stuck to the top plate, resettle plates and invert.

8. Lift the upper plate off. If bubbles arose, wet gel with 10% Acetic Acid and work them out. Pat dry gently with a Kim-Wipe.

9. If 35S or 33P nuclides are used:

A. Soak gel 15 min in 10 % Acetic acid. Pat dry.
B. Cover gel with Whatman 3MM paper. Lift off gel stuck on paper. Cover with plastic wrap.
C. Dry in vacuum gel drier for 20 min at 80 C. If soaked, dry 60 min.
D. If soaked, removed plastic wrap.
E. Expose to X-ray film.

10. If non-radioactive, stain with Ethidium bromide for 5 min. Illuminate with ultraviolet