Changes to the PCR buffer will usually affect the outcome of
the amplification. In particular, the concentration of MgCl 
can have a
profound effect on the specifity and yield of an amplification. Concentrations
of about 1.5 mM are usually optimal (with 200 
M each dNTP), but in some
circumstances, different amounts of Mg 
may prove to be necessary. For
that reason, every established PCR in this thesis was preceded by an
MgCl optimization assay. Generally, excess Mg will result in the
accumulation of non-specific amplification products and insufficient Mg
will reduce the yield.
The deoxynucleotide triphosphates are
usually present at 50 to 200 M of each. Higher concentrations may tend to
promote misincorporations by the polymerase and should be
avoided[96]. At 50 and 200 M, there is sufficient precursor to
synthesize approximately 6.5 to 25 g of DNA, respectively.
Taq polymerase is
available from a number of vendors. For amplification reactions involving DNA
samples with high sequence complexity, such as genomic DNA, there is an optimum
concentration of Taq polymerase, usually 1 to 4 units per 100 l.
Increasing the amount of enzyme beyond this level can result in greater
production of non-specific PCR products and reduce yield of the desired target
fragment.