oligo hybridization (degenerate oligo)

[Robert Saunders]

marc van de craen wrote:
> 
Dear Geert,

Try looking at Wood et al PNAS 82, 1585-1588

I found it very helpful for working out wash stringencies for oligo
hybridisations.

Robert

> Dear,
> 
> We want to hybridize two thousand of SELECTED cDNAs with 2 degenerate
> oligo's which only differ in one codon. One oligo (wtOLIGO) will
> entirely code for the cDNAs we are looking for. The other oligo
> (mutOLIGO) will contain specific mutations (at the level of the
> different codon) which will certainly not be present in the cDNAs we are
> looking for. By adjusting the washing conditions we want to select the
> cDNAs which specifically hybridize with the wtOLIGO and not with the
> mutOLIGO. We want to use the mutOLIGO to be sure that the hybridization
> conditions with wtOLIGO are optimal for specific cDNAs.
> 
> 1) Is it possible to do such experiments ?
> 
> 2) Can someone advice us how to design the oligo's and how to do the
> experiment (especially the washing    conditions are of concern for us)
> ?
> 
> 3) Is there literature describing analogous experiments ?
> 
> Geert