PCR/sequence through bad region

Chris Boyd cboyd at holyrood.ed.ac.uk
Mon Mar 27 06:51:18 EST 2000

Chris LaRosa <clarosa at biocomp.unl.edu> wrote:
: Betaine......is good for your problem.   You could also make a primers
: that sits on the bad g places.   make them ggggggggggggggggggg(bases in
: your sequence) or ggggggggggggggggggggg(N). Also CCCCCCCCCCCCCCC(bases
: in your sequence.OR N.   

Seems to me this is highly unlikely to work.  Usually you don't know how
many Gs or Cs there are.  Also, such primers are prone to anneal
slightly upstream of where you want them to and cause stuttering.  Have
you actually tried this method?

Best wishes,
Chris Boyd                      | from, but \    Medical Genetics Section
Chris.Boyd at ed.ac.uk             | not for,  /    MMC, Edinburgh Uni.,
http://www.ed.ac.uk/~cboyd                       EH4 2XU, SCOTLAND

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