Ambigous letters in PCR primer

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Ambigous letters in PCR primer

Postby Fab_chlt » Mar 13 2017 1:31 pm

Hi there,

I would like to use the PCR primer GS2a to amplify the bacterial glutamine synthetase gene. (from Hurt et al, 2001. Simultaneous recovery of RNA and DNA from soils and sediments. Appl. Environ. Microbiol. 67, 4495–4503).
The forward sequence is 5' AAGACCGCGACCTTPATGCC 3'. My question is: what does P stand for? Is it for the amino acid Proline, with the corresponding nucleotides CCN?

Thanks
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Re: Ambigous letters in PCR primer

Postby r.rosati » Mar 13 2017 6:21 pm

I humbly admit that I don't know. It's not IUPAC as far as I know...
Funnily enough there is a 2010 paper, "An extended IUPAC nomenclature code for polymorphic nucleic acids" (A.D. Johnson, Bioinformatics 2010) that suggests the use of extended IUPAC codes, and the only two letters this system doesn't use are P and Q.
And these primers are cited by other papers, so it must have a meaning. I'm eager to know what I'm missing, too...
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Re: Ambigous letters in PCR primer

Postby procper » Apr 12 2017 9:49 pm

I do't think that 'P' refers to proline in this context. I am not 100% sure but it could be a degenerate pyrimidine base. I found this old paper (PMC:22476--> "Polymerase recognition of synthetic oligodeoxyribonucleotides incorporating degenerate pyrimidine and purine bases.") where they slightly mention about this. I hope this helps.
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