An initial test of a methylation sensitive restriction digest did not work (large band rather than smear). The DNA used is precious and I would like to retrieve it (~120 ng). What would the best method of retrieval be? I'm contemplating magnetic beads, but wonder if something simpler might work well. I'd rather not do phenol-chloroform, and worry about losing product in a spin-column based pcr purification. Any tips?
Hi
you should maybe try silica-gel based extraction kits like ~> https://www.qiagen.com/us/shop/sample-technologies/dna/genomic-dna/qiaex-ii-gel-extraction-kit/#productdetails
however recovery yield is mostly not very satisfactory
Hi Stephanie,
If you need to recover more DNA, the better option is the phenol-chloroform & ethanol precipitation. Since you are reluctant with it, you can heat inactivate the enzyme & directly go for ethanol precipitation.
if you do use direct ethanol precipitation you will increase the yield ( minimise losses) by adding some glycogen or rna as a co-precipitant which increases the bulk of the precipitate and traps all of the precipitated dna
Heat inactivation is mentioned. I've used 3 enzymes, one of which cannot be heat inactivated--is inactivation necessary before trying an ethanol precipitation?