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Amplified Regions
The P and M primer sets are designed to amplify a differentially methylated site
present at the CpG island of the small nuclear ribonucleoprotein-associated
polypeptide N (SNRPN), a candidate gene for Prader-Willi Syndrome. The
amplified region is defined as the sequence between the 3' nucleotide of the
sense primer and the complement of the 3' nucleotide of the anti-sense primer
for each primer pair. The nucleotide numbering system is that used in the
GenBank submission identified by the accession number L32702.
"Hot Start" PCR
The two sets of primers used in the CpG WIZ Prader-Willi/Angelman
Amplification Kit 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, it is recommended that a "hot start" enzyme be used.
Normal Control DNA
The normal control contains DNA from both maternal and paternal homologs
which means that both methylated and unmethylated SNRPN sequences are
represented. Therefore, PCR products will be obtained after the bisulfite
modification of the normal control DNA when using either the M or the P
primer sets. The M primer set will generate a 174 bp product while the P primer
set produces a 100 bp fragment. Multiplex amplification is feasible since the
fragment sizes are sufficiently dissimilar.
Specificity of the Assay
The specificity of the CpG WIZ Prader-Willi/Angelman Amplification Kit is
shown in Figure 3. With a complete chemical modification reaction, P primers
amplify only unmethylated DNA (100 bp, lane 1) and M primers amplify only
methylated DNA (174 bp, lane 2). The smaller bands present in the lanes where
the M primer set was used in the PCR reaction represent excess primers.