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Why would the identical amino acids region of certain specie

Genetics as it applies to evolution, molecular biology, and medical aspects.

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Why would the identical amino acids region of certain specie

Postby TToe » Mon Feb 18, 2013 10:37 am

Why would the identical amino acids region of certain species be used as a basis for a primer design?


I know they share homology and are very conserved but why is it used as a primer?
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Postby JackBean » Mon Feb 18, 2013 1:06 pm

Because if the amino acids are identical, the DNA sequences are probably also very similar (but does not have to be identical!), thus primer annealing to this region may be used for several species. It can be used either as unspecific primer for known species or it can be used even for so far unsequenced species.
http://www.biolib.cz/en/main/

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Postby JackBean » Mon Feb 18, 2013 3:51 pm

OK, so you have DNA sequences from related species which are somewhere diverse, somewhere are identical. For example the region coding for active site will be probably conserved, while some loops on surface of the protein will be divergent. Both on DNA and amino acid level.
You can design primers on the divergent regions and then they will be species-specific, because they will bind to the sequence of only one species. On the other hand, you can design primers to the region which is the same in all species and then the primers will give signal from all species.
You can use it for detection of one taxon, say you will want to know whether Klebsiella bacteria are present in your sample. Than you will use some primers which amplify some specific gene. Or you can use it for detection of homologous protein in other species as you described in the other question.
http://www.biolib.cz/en/main/

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