Need help purifying DNA oligoes - (Nov/04/2005 )

Hi all,

So, I purchased a 45-mer and 22-mer DNA oligos. I annealed them and ran them out on a gel to make sure the annealing was complete. The next step I have to do is incorporate a nucleoside analog onto the 22-mer primer. The paper I'm following said that after the incorporation they did a gel purification, but they did not say exactly how they did this. I looked to see if there were any kits available to gel purify such small oligoes, but I could not find any. So, I was wondering if anyone might have any advise on how to get rid of the agarose after I run my DNA on a gel?

Thanks,
Greg

there is an old method involving punching a tiny hole in the bottom of a 0.5mL eppy tube, packing it with sterile glass wool, and putting this tube inside a 1.5mL eppy tube. you can put your slice from the gel over the glass wool and spin the nested tubes. This removes the agarose; your sample is liquid in the bottom of the larger tube. then you do a standard etoh/oAC precipitation to clean up your DNA.

I don't know why this would not work for oligos; anyone else have any ideas?

there should be a lot of kits .... I use GelEx from molzym. quaigen and several other companies definitly offer some. getting rid of agarose is easy, most of these kinds contain agarase (enzym digesting agarose) or chemicals, that do the same. or use the procedure amikins described, it also works for sure, but needs some handcraft skills

but considering the realitively small size of your oligo, may be it would be better to do a polyacrylamid gel and purify from that. a procedure for that you can find with google, or ask again, and i'll check some old data i have