degenerate oligo design

Mon Dec 6 12:49:03 EST 1993

Dear Netters,
      I wish to design a degernate oligo based on peptide sequence for
screening a genomic library.  I wondered if anyone could give me an idea as
to the relative importance of number of possible combinations vs number of
known bases.  I have the follosing options:

          20mer     2048 combinations     14 known bases
          17mer      512 combinations     12 known bases
          14mer      128 combinations      9 known bases

Is it better to go with more known bases and hope that a lot of the degenerate
combinations will hybridize anyway?  My feeling is that the longer oligo would
give me more room to mess with hybridization conditions.

More information about the Methods mailing list