How to name primers? - Any official nomenclature systems to name primers? (Dec/18/2008 )
Are there any official authorities or regulations to designate the names for primers?
Or is it soly up to a person who designs primers?
I wonder how my HIV RNA primers have been named like 1869F, 1468R..
It is up to the person who designs/uses them. It is merely for reference on what they prime, when they were ordered, etc. F and R usually refer to the forward primer and reverse primer.
There's no official naming convention, but I would assume that those names refer to the orientation (Forward and Reverse) and the location of the primers on a specific region of DNA. Different people use different conventions as to whether the number is the 5' or 3' end of the primer, but I think the 5' end makes more sense. Then, there is the issue of how you denote the 5' overhangs for adding sequence, and there is little agreement on that.
As I've gone through graduate school, I've named all of my primers in ascending order and kept an Excel spreadsheet with their sequences, Tms, and uses. It's helped me keep it organized and makes it easy to pass on to others in the lab.
Your lab may have a specific way they name theirs.
It would be a lot easier if there was some standardization in this I believe...
It all dependent on lab system, so the people came later can understand what are those primers for.
The loading control I used is hHPRT-F101 and hHPRT-R572.
h for human (we also test mouse and other species)
HPRT is the gene name.
Number identify the primer 5' end location on the sequence from data base.
From the number 101 and 572, I can easily know the size of my product is 472 bp.
As long as it is clear to OTHER PEOPLE, it does not matter how you name your primer.
We do also have Excel sheet to identify other detail of those primers, but our purpose is to identify can this primer used in different species.