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Context dependent polymerase errors [was Re: Sequence variations]

Robert Bradbury bradbury at sftwks.UUCP
Fri Dec 11 19:01:10 EST 1992

In article <Bz1w8o.ExA at ncifcrf.gov> oberste at fcs260c.ncifcrf.gov (Oberste) writes:
>Since a PCR-induced base change is propagated through subsequent cycles,
>it is important to collect and compare sequence from independent PCR
>amplifications. It would be extremely unlikely to see the same artefact
>in independent amplifications.
I'm not sure that I agree with this.  Polymerases will incorporate
improper bases depending on the surrounding context.  If a
polymerase is inclined to make a mistake once, it might make the 
same mistake again.  A much better solution IMHO is to do the PCR
with several different polymerases.  The polymerases tend to show
different misincorporation characteristics and it would be less
likely that different polymerases would make the same context
dependent errors.

Another thing to consider is the error correction capabilities
of the polymerase.  Those without 3'-5' exonuclease activites
have an error rate about 100x those with this exonuclease

Robert Bradbury			uunet!sftwks!bradbury

Death is an imposition on the human race, and no longer acceptable
				Alan Harrington, The Immortalist (1969)

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