
8
“Hot Start” PCR
The three sets of primers used in the CpG WIZ Methylation Assay are derived
from sequences closely related to each other, which introduces the possibility of
mispriming. In order to avoid this and other PCR-related artifacts, "hot start"
PCR is recommended. "Hot start" PCR permits the Taq polymerase to begin the
reaction only after the template and primers are in single-stranded form.
There are several modifications of the standard PCR protocol which allow a "hot
start" to occur. In one scenario, the PCR reaction mixture excluding the
polymerase can be overlaid with mineral oil prior to heating to 95°C. At the end
of the incubation, the enzyme is pipetted directly into the mixture under the
mineral oil. A second method involves the physical separation of the polymerase
and the rest of the PCR mix with a wax bead. The enzyme combines with the
rest of the reaction mixture only after the wax melts. In another variation, an
anti-Taq antibody inhibits the polymerase during reaction setup by forming a
complex with the Taq enzyme. Taq polymerase becomes active when the
complex is abolished due to antibody denaturation during the 95°C incubation.
Alternatively, a "hot start" enzyme can be used. Refer to the manufacturer's
instructions for enzyme activation protocol.
Note:
Do not use a polymerase with 3'-5' exonuclease activity (i.e.
proofreading).Do not use a wax bead that contains Mg
2+
. Any extra Mg
2+
added
to the reaction mixture produces suboptimal results.
Genomic Control DNAs
The methylated (red cap) and unmethylated (white cap) control DNAs must
undergo bisulfite modification prior to PCR amplification using the
CpGenome DNA Modification Kit (S7820). When used with their respective
U and M primer sets, a single PCR product of an expected size is obtained in
each case.
W control genomic DNA is used in the PCR and is NOT to be used in the
chemical modification step. When used with the W primer set, it is a positive
control for PCR amplification. Failure to generate a PCR product indicates a
general failure in the PCR reaction.