Oligonucleotide probes

metzler at sara.cc.utu.fi metzler at sara.cc.utu.fi
Tue Dec 28 09:05:54 EST 1993

Hi netters,
	I want to look for genes which may have low homology to some
known protein sequences. I am thinking about using oligonucleotides that are
based on the sequence of regions of the protein which are most conserved.
We need to make oligos which are ambiguous in the third position (usually)
and I don't know if there is a best strategy for doing this. For instance,
assuming you have several conserved regions to choose from, you would prefer
one containing amino acids like Met and Trp, which have only one possible
codon. Are there any other things to keep in mind with this strategy?
And what about good hybing conditions, not too stringent but not so low
stringency that you get too much background?
Does anyone have a reference that can give me some hints about good
ways to do this? 
Mary Metzler
Mary C. Metzler,                       |  Internet:  Metzler at Sara.CC.Utu.Fi  
Department of Botany,                  |  
University of Turku,                   |  This space to be witty until I think
Turku, SF-20500                        |  of something filled... oh yes.
Finland.                               |  a jelly donut.

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