Re: Why is salmon sperm used in a Southern Blot?

Chan:
     That is a good question. You have a couple of questions there, and I 
will see if I can rephrase them.  First, you want to know why Salmon sperm 
DNA is used in a Southern blot, and second, why Salmon sperm DNA, and not 
African Fire Newt DNA???
     A Southern blot is used to detect an interaction between two pieces 
of DNA.  A northern blot detects a RNA/DNA interaction, and the western 
blot is used to detect protein/protein or protein antibody interactions.  
Essentially, in a Southern, you separate out your DNA of interest on 
something called a 'gel' and then transfer the gel to a type of paper to 
which DNA sticks.  You then wash the paper with a different piece of DNA, 
called a 'probe' that you know the sequence of typically, and it is 
labelled in some way and if it sticks to its complementary piece of DNA of 
the paper, you can detect this, and then know that that piece of DNA was 
present in the sample you ran on the gel.  There are two problems with 
this.  First, is that the paper will stick any DNA, even your 'probe' and 
would therefore not concentrate at its AT GC complement, but everywhere on 
the paper and would be detected all over.  Second, is that this 
interaction is specific, but not perfect.  So, if we have some DNA that it 
also sticks too, this would generate a signal in the wrong place, a false 
positive.  
     The sperm DNA fixes these problems.  After we transfer the DNA to the 
paper, we wash it in lots of the sperm DNA.  All of the sperm DNA sticks 
to all of the remaining places on the paper and prevents any additional 
DNA from sticking anywhere to it.  It is as if you colored a piece of 
paper black, you wouldn't have any place left to color it yellow.  So now, 
the only places on the paper that can stick DNA, are pieces of DNA already 
stuck to the paper themselves.  
     Secondly, sperm DNA is heterologous, which is to say it is a mixture 
of lots of different DNA sequences.  So, if we had a probe that interacted 
with multiple piexes of DNA, it would probably find a similar match 
somewhere in the sperm DNA and make the false positive we mentioned 
earlier.  By running sperm DNA with our sample, we can look for bands of 
sperm DNA that interact with our probe.
     Your next question, was why salmon sperm DNA?  There are two 
answers.  First is that salmon sperm DNA is different from what most 
people are studying.  You generally don't want your non specific DNA to 
come from the creature you study, like humans, because it will contain the 
DNA you are looking for as well.  I suspect that salmon researchers don't 
use salmon sperm DNA for that reason, but something else.  Secondly, is 
that thanks to a massive aquaculture industry in America, we can get lots 
and lots of salmon sperm very cheaply, which is also important.
     I hope this answers your question, thank you for taking the time to 
write us.

-Matt-
 
Moderator's Note:
In European laboratories, they use herring sperm DNA, again because of minimal 
crossreactivity and, more importantly, availability.