I have a mixture of a PCR fragment and Salmon Sperm DNA. I'd like to reuse the PCR fragment and get rid of the genomic DNA. Is there a RE similar to DpnI that cuts eukaryotic DNA?
Thanks!
Honestly I'm not aware of it, mammalian genomic DNA can be methylated on GpC islands, but only in regulatory regions, so most of it is not.
My suggestion would be to run your mixture on agarose gel and extract your PCR fragment.
Thanks for your quick reply! Actually I need quite a lot of the DNA fragment for my experiment (i.e. 500 ug = 1 nmol). I could imagine that that's a little too much for my little gel to separate
Well, yes, you are right, extracting from gel 0.5 mg of DNA is not possible.
I guess it might be useful to have more details, such as the size of your amplified fragment and estimated amount of Salmon sperm DNA mixed with your sample (did you amplify from it? then it could be there in negligible amounts after amplification...), but in general you might want to use a biochemical/chemical approach, for example a filtration method, with an appropriate size cut-off, or a preparative chromatography column...
I would suggest you go with Derya's answer, there are a lot of commercial kits to assist with this process. Simply cut the band with your required DNA amplicon out of the gel and follow the procedure, using this as template DNA in future PCR cycles should easily help you achieve the required concentrations.
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