BIONET DNA Sequencing Survey

pmiguel at pmiguel at
Sat Jun 19 12:42:11 EST 1993

In article <19JUN199308260889 at>, broe at (Bruce Roe) writes:
>I have a tendency to think about bands in all 4 lanes as being due 
>to "template compression" i.e.  secondary structure, since "product
>compression" also is due to secondary structure ( fold back )
>in the synthesized strand.
  Yeah, but calling template secondary structure "compression" is 
confusing.  "Product compression" is seen as bands compressed together on 
the sequencing gel, thus the name.  Extremely bad compression could look
like or be accompanied by what you call "template compression"  -- bands 
across all four lanes.  I call this "fall-off" because it is so refered to in 
the Sequenase manual, because it makes sense to me and, probably more 
important isn't easy to confuse with "compression."
  I'm not just quibbling over nomenclature here.  If you have a compression 
you need to run a gel with formamide in it or do rxns with dITP or dazaG 
replacing dG.  If you have fall-off you need to increase the temperature of 
your extensions or use SSB to eliminate template secondary structure.  


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