Our lab has extracted bacterial DNA samples using Qiagen DNeasy kit and eluted the samples in AE buffer. However, this buffer contains 0.5mM EDTA not suitable for downstream application. Any ideas on how to remove the EDTA or decrease it to the required amount for downstream applications (not more than 0.1mM)?
You could precipitate the dna with salt ethanol possibly with a co precipitant like linear acrylamide or glycogen if the starting amount of dna is already low. Then wash the salts away with 80% etog and redissolve in water
In our lab we use the following protocol to precipitate pDNA and change the buffer:
-add to 1V of your pDNA 0.1V of 3M NaOAc and 2.5V of 96% EtOH
-incubate 30 mins on -70C
-centrifugate 30-40 mins +4C 13,000rpm
-wash the pellet with 75% EtOH
-let it dry and dilute the pellet in H2O.
in case you have large volume of pDNA you can precipitate pDNA with 0.7V of isopropanol, centrifugate 15,000g +4C 30mins. Then wash the pellet with 70-75% EtOH, centrifugate for 5 min at 15,000g and let the pellet dry. After that you can dissolve your pellet in water
and for the future you might want to elute the purified dna in water not buffer from your columns