Neomycin resistance sequence - (Jan/24/2013 )
I have a non-commerical plasmid which I am trying to figure out if it has a Neomycin(G-418) resistance cassette or not. I thought one strategy would be to align the nucleotide sequence of Neomycin with the plasmid's. Unless I am confused, I found more than one sequence for Neomycin resistance. Would anyone know which sequence exactly should I look for within my plasmid? or any other ideas?
Neomycin belongs to the group of aminoglycoside antibiotics, so does G-418 (also known as Geneticin). The "usual" Neo-resistance comes from an APH3' resistance cassette (phosphorylates the 3' OH in aminoglycosides). Pay attention that there are other resistance cassettes which confer resistance to several aminoglycosides such as APH2'', AAC2 etc. This means not all resistance cassettes confer resistance to the same aminoglycosides, e.g. Tobramycin has a 3' H and won't be phosphorylated by APH3' and remains active.
A good overview you can get in this Minireview: Aminoglycosides: Activity and Resistance. Mingeot-Leclercq et al., AAC 49(4) p. 727-737, April 1999
If you have the sequence of the Neomycin resistance cassette you should simply BLAST and you'll know immediatly which one is yours.