I wonder how can I know when I want to purify my DNA (Cloning Vector) after digestion with restriction enzymes, which method to use (gel extraction or purification with FDA column)? Is it no problem if I purify my DNA with column instead of doing gel extraction? If you exactly the conditions for each purification method, please let me know and it would be great help to my experiments. Thanks.
It depends upon what you are trying to separate your DNA from. If the objective is to separate the DNA from enzymes or buffers etc, then a column would be fine. But if you are trying to separate an insert band from a vector band, then you need to use a gel. A column will not provide size separation of similarly sized fragments in the typical range you would have.
Both methods can work. As Michael J. Benedik states above, if you need to remove other DNA sizes, then you'll need to run a gel (then excise and purify the band you want). Regardless of the method you choose, I would highly suggest running your sample (either all or a test aliquot) onto a gel to make sure the cutting worked before you move forward with purification.
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