DNA polymerase fidelity and the polymerase chain reaction. - Ozyme

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not in large excess over the total concentration
of dNTP substrates, and be
buffered to -pH 6 (70~ using Bis-Tris
Propane or PIPES (Table 2). These buffers
have a pK a between pH 6 and pH 7
and a small temperature coefficient
(ApKa/~ allowing the pH to be
maintained stably throughout the PCR
cycle.
For amplifications in which fidelity
is the critical issue, one should avoid
the concept that conditions generating
more DNA product are the better conditions.
Reactions that optimize fidelity
may be relatively inefficient for
amplification. The total number of
cycles should be kept to the minimum
necessary to produce a feasible amount
of product DNA for the desired use.
Thus, although using low pH, low
Mg 2+, and/or a low concentration of
dNTPs may not produce an impressive
amount of amplification product as
visualized on an ethidium bromide
stained-agarose gel, these conditions
may provide an adequate amount of
DNA for cloning purposes. Using a
small number of cycles will also minimize
the contribution of mutations
resulting from DNA damage at high
temperature. The DNA sequence of
several independent clones from the
final PCR population should be determined
to verify that the original DNA
sequence has been maintained during
the amplification process. Ideally, the
clones should be derived from separate
PCR experiments to minimize the risk
of overrepresentation of early polymeruse
errors.
The fidelity of DNA synthesis in
vitro is limited by the least accurate
reaction that occurs. For example, the
T~ mispair is one of the most frequently
produced and most easily extended
base substitution error.(35) Even
under high-fidelity reaction conditions,
most of the Taq polymerase errors
were the result of T~ mispairs
that led to A'T~G'C transitions.(13)
Therefore, the upper limit for Taq polymerase
fidelity will be the frequency
with which the enzyme creates this
mispair. In general, this limitation is
not restricted to a particular mispair.
The sequence of the target DNA will
have a profound influence on the generation
of mutations. Thus, the least
accurate reaction may be the result of
an exceptionally high error rate at a
particular nucleotide sequence, since
the phenomenon of "hot spots" for
polymerization errors has been clearly
established.(16)
ACKNOWLEDGMENTS
We are grateful to Drs. Theodora
Devereux and Neal Cariello for helpful
comments and critical evaluation of
the manuscript. We would also like to
thank Drs. Myron Goodman, William
Thilly, Lucy Ling, Pekka Mattila, and
Neal Cariello for providing results prior
to publication.
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