Hi! Greetings from...work. This week I'm designing primers--little chunks of DNA that seek out and bind to their complimentary sequences in busted up genomic DNA samples--so that I can amplify two genes that are missing from our Complex I subunit set.
One of those genes hasn't been sequenced in Fundulus or Danio, so I'm making some degenerate primers for identifying it. Whatcha do with those, is make an alignment of protein sequences from closely related organisms--other fish in this case--and figure out what the possible combinations of nucleotides are for the amino acids in highly conserved regions, and then design a primer from those.
Most amino acids are coded for by more than one set of nucleotides, so you need more than the typical four letters--A,C,T,G--to describe them. The degenerate code contains letters that mean things like "any thing but T" or "A and C only". So, while I was digging around in my protein alignment, I came across this potential primer, which I think may be the best one ever designed:
GAY MGN GAY AGN GAY
Too bad it's so repetitive...
2 comments:
The nature is great in its wisdom!
so it reads gay management gay again gay? well if there is a gay gene i think you found it. or maybe just the old english happy manager gene.
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