For an upcoming experiment I would have two kinds of DNA fragments in a sample after a particular reaction step: First there would be fragments of a length of approx. 170 bps and then there would be Fragments of a length of approx. 270 bps or more.
I would like to maintain all fragments with a length of 270 bps or more and throw out all fragments with a length of 170 bps.
Of course, I could run everything on a gel and collect just those bands above 170 bps.
However, I am wondering whether there is something more elegant to reach that aim. For instance, we could use a filter that collects just those fragments with a size of 200 or 250 bps or more and those fragments with a smaller size flow through the filter.
Is such a thing possible and if so, how? Or would you suggest something else?
Many thanks for your support in advance!
I do not think that filters would be able to distinguish between 170 and 270 bp. What you want is a capillary electrophoresis system. However, they are expensive so you would have to justify the extra expense if you do not already have one in house. In my experience, gel purification is quick and easy.
Dear Tobias, Perhaps you can try the CHROMASPIN column from clonetech. They have different columns with different cutoff specifications. These are small columns and easy to use. But be aware as with columns you should take in to account that you might lose some samples. But offcourse you can concentrate the DNA afterwards if required.
Is there any possibility that the shorter fragment has some restriction sites that are not present in the longer fragment?
Now I am curious: how have you generated two sizes of DNA fragments the individual components of which are of different sequences??
Affinity purification using a short capture oligo (or oligos) would in principle be one approach to isolating what you want, but not if the sequences are different!
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