Small DNA fragments, which electrophoresis shoudl i choose? - (Jan/14/2008 )

My PCR products are small DNA fragments(less than 300bp), than I want to digest with restriction enzymes.
Which electrophoresis is better, PAGE or Agarose gel electrophoresis ?

Waiting for your replies. Thank you !

By the way, I'm new to this so any help would be appreciated.

using a 50bp dna ladder and a 3% agarose BET gel, iwas able to discriminate dna fragments between 20, 80, 100, 220 and 400 (my sizes of interest).

PAGE is very good for resolution, but less good for separation and extraction. Agarose gives a lower resolution, but is easier to extract the fragment from. You use what you need.

I would use agarose gel electrophoresis. I have used agarose gel to run 100bp pcr product digest.

I would also use agarose, 3-4% Metaphor or Nusieve will resolve 10 bp differences with little difficulty.

Small fragments of RNA, ssDNA or dsDNA can be easily passively eluted from 6 - 12% polyacrylamide gels. Higher percentage gels will require a crush/soak approach to release the fragment.

Cut out the band of interest and elute in a low-binding polypropylene microfuge tube in water or 0.3 M sodium acetate (use sodium acetate if you are going to ethanol precipitate).

Rotate the tube at room temperature for 4 hours (you can rotate over the weekend without any problem).

Spin briefly and transfer the supernatant to another tube. If gel fragments are present, spin sample through a Costar Spin-X cartridge. Ethanol precipitate if desired with linear polyacrylamide carrier. Recovery is 95% in my hands.

Thanks a lot !