How do I separate double-stranded from single-stranded oligos while still getting good recovery?
The best way to distinguish and separate double-stranded oligonucleotides from those that are single-stranded is by running them on a non-denaturing electrophoresis gel. At IDT, we would use a 12−15% polyacrylamide, 1X TBE gel. The lack of denaturants (e.g., urea, SDS) keeps the double-stranded oligos intact. You can then excise this product band from the gel and extract the oligonucleotides from it.
Please note, however, that no matter how careful you are, you will lose some yield during the extraction process. Electroelution will return the most full-length product from the gel. Though not quite an effective as electroelution, dialysis can also be used.