PCR clone a gene with known 3' end only - (Aug/23/2006 )

hello there,
I am completely new here but with a very frustrating problem.I want to clone a gene but I don't it's exact sequence.I have the sequence of 3' end of that only.Please suggest the best and cheapest way to clone that dude.I would feel very grateful if you give the suggestion on me e-mail..sanjay_singh765@yahoo.com.
thanx
sanjay

hi
If the gene you're dealing with has a sequence that's highly conserved throughout organisms, or a very conserved sequence in the 5' end of the gene, you could try designing degenerate primers for PCR.

I'd prefer RACE to get the full length and starts from there though.

you could probe a library with the known portion of the sequence, if you have a library available? then you have clones containing the gene, for future work

You could try inverse PCR. Cut genomic DNA with an enzyme which does not cut in the region you know about. Re-ligate the resulting DNA. Make two outwardly directed primers at the ends of the region you know about, and PCR the ligated DNA as a template. The band you get will show the context of the region you have sequence for. Rinse, lather, repeat as necessary. The GC content of your organism will determine the best choice for your enzyme, and the length of its recognition site.