How can I tell if my oligos successfully annealed?
The hybridized oligos or DNA duplex can be run on a non-denaturing gel wtih appropriate molecular weight markers. Alternatively, run the duplexed oligo side by side with single-stranded oligo. If annealing was successful, the double-stranded band will be shifted up from the single-stranded band. Use UV backshadowing or a stain such as SYBR® Gold to visualize the bands. Ethidium Bromide may not sufficiently stain the single-stranded DNA to make it visible.