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I am reading a paper on a certain marine microorganism that can eat alkanes and therefore might be useful for cleaning up oil spills, etc. This sentence struck me as odd (although I am sure that the answer is pretty simple):

Using the same probe, Southern blotting analysis showed that there was only one copy of alkB1 in the B-5 chromosome.

I realized that I don't know how Southern blotting can tell you about copy number. Can someone help me on this?

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    $\begingroup$ please edit your question to include a link to the paper, so we can see everything in context. $\endgroup$ – MattDMo Jan 21 '14 at 20:33
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This method is commonly practiced. Atleast I see the people working with zebrafish transgenics using it.

When you shear the genomic DNA or do a restriction digestion, you are likely to get fragments of different sizes. It is highly probable that the two (or more) locations harboring a copy of the DNA element are a part of fragments with different sizes. So on the blot you'll get two bands.

But as I said this test relies on probability that the two fragments are dissimilar in length. Therefore, southern blot should not be considered as an absolute test to determine copy number. Inverse PCR, FISH, etc can be used to determine copy number.

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