how to design a kozak sequence in front of the start codon
Posted 26 September 2011 - 06:35 PM
i am currently trying out a subcloining with a recombination system, and honestly this is my first experience with it, so i really need to get help from you guys, any advice will be appreciated much.
i am designing a primer of a kozak sequence followed with the start codon atg. I have read some literature saying that the best kozak sequence is gccgccacc , but i rarely see any plasmid has this kozak sequence, of course some other kozak sequences may also work perfectly. my question is is there any other rules to follow to design the kozak sequence in front of atg, if gccgccacc is the best kozak, why people chose other kozak rather than this? and do i need to put any linker between atg and kozak?
please help me out on this issue, i appreciate much.
thanks in advance
Posted 27 September 2011 - 05:56 AM
The other thing you have to think about is what system you are working in. Bacteria? Yeast? Insect Cells? Mammalian Cells? This does make a difference, since the "Kozak sequence" is actually different depending on what cell type you're in. I would recommend you read this paper on start codon context to get a feel for what I'm talking about:
Cavener, D.R., and Ray, S.C., 1991. Eukaryotic start and stop translation sites. Nucleic Acids Res. 19, 3185‑3192
Best of Luck.
Edited by allynspear, 27 September 2011 - 06:02 AM.