How do I separate double stranded and single stranded oligos while still getting good recovery?
The best way to separate single-stranded oligonucleotides from those that are double-stranded is by running them out on a non-denaturing electrophoresis gel (we would use a 12-15% polyacrylamide, 1x TBE gel). Do not add urea or SDS to the gel. You can then run the gel and remove the band corresponding to your double-stranded product from the gel. Please note, no matter how careful you are, you will lose some yield during the purification process. If you feel the additional purification is absolutely necessary, try using electrolution to remove the full length product from the gel. This will lead to the largest possibly mass recovery. You can also dialize the gel to remove the oligo, but this will not give you quite as much yield as electrolution. No matter which method you try, make sure you are using a non-denaturing gel for the purification process. For additional information on electrophoresis protocols you may want to visit www.protocol-online.net.