Touchdown PCR with Degeneracy?

Fred Boyd, Ph.D. fredboyd at
Tue Oct 26 13:23:05 EST 1993

Does anyone have any thoughts on the use of "touchdown" PCR for
identification of previously unidentified members of classes of genes.  As
I understand it, this involves selective amplification in early rounds of
sequences which have high homology to the degerate primers via inital high
annealing temperature.  After a couple rounds of amplification the
annealing temp is dropped a couple degrees and so on until one reaches a
relatively low annealing temperature were the final 20 or so cycles are
carried out.

My concern is that one is selecting for those sequences most homologous to
the primers and probably biasing against new products.  Any better ideas?

Fred Boyd, Ph.D.                  Voice- 612-624-8150
Lab. Med. Path.                   Fax- 612-616-2444
Cell Biol. Neuro.                 Lab- 612-624-8154
Box 609, UMHC   
University of Minnesota           E-Mail  fredboyd at
Minneapolis, MN   55455

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