PCR and Strand Displacement

Dr. M.D. Jones mjones at crc.ac.uk
Thu Jul 28 04:20:28 EST 1994


Hi Netters

I have a query about PCR and Strand Displacement.

According to the literature, Taq DNA polymerase does not possess strand displacement
activity.  In other words, if the pol complex was extending on a large ss DNA
template, which had a downstream duplex region (which is perfectly base paired) the
enzyme would stop !

----------pol->           -----------      yields  --------pol->-------------
-------------------------------------              ---------------------------

So, during PCR amplification of a large DNA fragment (>3,000 bp) at every heat
denaturation step at 94C, are both DNA strands fully denatured and separated,
so that primer cann anneal to its target sequence and thud yield PCR amplification ?

Or, are the two strands only partially denatured, allowing the primers access to their
target site.  Is the this already displaced partial duplex amplifiable by Taq DNA pol ?

       ------\
              \
-----pol->     \------------------        PCR amplifiable
----------------------------------

I would be very grateful for people's views on whether duplex DNA is completely denatured
at every cycle in PCR or not.

Many thanks


Mick

___________________________________________________________________________________________
Mick Jones                        Tel: +44-81-740-3328
Department of Virology            FAX: +44-81-743-8331
RPMS, Du Cane Road                Email: mjones at rpms.ac.uk
London, W12 ONN
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"Smoke me a kipper, I'll be back for breakfast."
Ace Rimmer (Red Dwarf)
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