ssDNA purification - (Sep/20/2006 )

I try to select an DNA aptamer for a protein. For this purpuse obviously i need a single stranded DNA. To get ssDNA i carry out an assymetric pcr and think to isolate ssDNA band from agarose gel but i have some problems. Since pcr product is too small (100bp) i use 2.5-3.0% agarose gel. I've tried many gel extraction kits they are even inefficient to purify dsDNA at that size. What can be the solution?







Tahir Bayrac

Have you tried ultrafiltration, like filters designed for microcentrifuge tubes?

yep most DNA gel extraction kits are based on silica column purification. They all have a cutoff of>150-200bp of dsDNA.
Have you tried bead based purification methods?