Primer design reference positions

[fungs]

Hello,
this might seem like a very basic question but I could not find a clear answer, yet. So I am hoping that anyone here is familiar with this matter.

I'm dealing with 16S primers for hypervariable regions. There are some primer variants like '967F' that are published in literature and used to amplify these regions. I know that positions are usually given in terms of E.coli genome positions. This would mean that the Primer 5' start position is at the 967th base of the corresponding reference E.coli 16S rRNA gene? Then, I would like to know which E.coli genome and which rRNA copy in the genome is specifically taken as reference. There are so many E.coli sequences in public databases...

Yes, I could probably align the primers to any of the reference sequences but I would like to know the definition.

Thanks for your help, if you happen to know.

J.

[nmcnulty]

Primer design reference positions

I found your post while searching around for an answer to the same question. After a fair bit of digging, I found some articles suggesting that the E. coli 16S numbering scheme is based on the sequence reported by Brosius et al. in PNAS in 1978:

http://www.pnas.org/content/75/10/4801.abstract?ijkey=1655271ac8e7b6d00771eeb3d4d4941c4e5c02e1&keytype2=tf_ipsecsha

For completeness, here is one of the articles claiming this is the scheme used:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC557567/pdf/emboj00311-0162.pdf

[fungs]

Thx

Never thanked you for your answer. Thx!