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LCR primer design

Ed Canning canning at sasa.gov.uk
Mon Nov 6 08:14:01 EST 1995

I'm in need of help from anyone with experience
in LCR primer design.  I'm new to this protocol
but am intrigued by the seemingly universal desire
of LCR primer designers to have a single base
overhang at the 3' end to reduce non-specific
ligation.  I can't seem to find any paper with 
a comparison of blunt end primers and overhanging
primers, just papers suggesting this may help
reduce background and referring to a similar paper.
Is it that a single overhang improves specificity
when looking at/for point mutations, the mismatch being
at the 3' end, and this now being part of LCR dogma with
regards background?  I'm intending to try using LCR for 
virus detection, comparing with a working RT-PCR, and as
such have no point mutation.  Cloning experience would 
lead me to design blunt ended primers rather than with
overhangs to reduce non-template ligation, not the other
way round.  Any help at all will be gratefully received
before I raid the coffers to pay for the things.


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