Designing primers from amino acid sequence - cloning problem (Mar/02/2005 )

Hi All,

Request for help...
I have partial amino acid sequence of a protein from a snail. I need to clone the corresponding gene from a cDNA library based on primers designed from the aminoacid sequence (backtranslation). Can anyone help me on how to design primers from aminoacid sequence? The probles is that since there are multiple codons for aminoacid, i do not know which one to take.

Thanking you
mman

Hi Mman,

Fast PCR can design degenerate PCR directly on amino acid sequence. This program can be freely downloaded and installed into your desktop.
http://www.biocenter.helsinki.fi/bi/bare-1_html/oligos.htm

Cheers.

mman's right. degenerated primers should be the right thing for you. another possiblity would be to check the protein databases if there's this or a similar aminoacid sequence known, and if it is, you can see if you can find the according DNA-sequence. Small AA-Sequences can be searched at

http://www.ncbi.nlm.nih.gov/BLAST/Blast.cg...ET_SEQUENCE=yes

but I'm sure you have already thought of that.

mike

Its been my experience that work involving snails moves very slowly.

KCrunner