Bisulphite differential denaturation PCR for analysis of DNA methylation.
Differential denaturation during PCR can be used to selectively amplify unmethylated DNA from a methylated DNA background. The use of differential denaturation in PCR is particularly suited to amplification of undermethylated sequences following treatment with bisulphite, since bisulphite selectively converts cytosines to uracil while methylated cytosines remain unreactive. Thus amplicons derived from unmethylated DNA retain fewer cytosines and their lower G + C content allows for their amplification at the lower melting temperatures, while limiting amplification of the corresponding methylated amplicons (Bisulphite Differential Denaturation PCR, BDD-PCR). Selective amplification of unmethylated DNA of four human genomic regions from three genes, GSTP1, BRCA1 and MAGE-A1, is demonstrated with selectivity observed at a ratio of down to one unmethylated molecule in 10(5) methylated molecules. BDD-PCR has the potential to be used to selectively amplify and detect aberrantly demethylated genes, such as oncogenes, in cancers. Additionally BDD-PCR can be effectively utilized in improving the specificity of methylation specific PCR (MSP) by limiting amplification of DNA that is not fully converted, thus preventing misinterpretation of the methylation versus non-conversion.
Rand
Keith N
KN
Preventative Health Flagship, CSIRO Molecular and Health Technologies, North Ryde, Australia.
Mitchell
Susan M
SM
Clark
Susan J
SJ
Molloy
Peter L
PL
D019313:BRCA1 Protein / Q000235:genetics; D004247:DNA / Q000737:chemistry / Q000378:metabolism; D019175:DNA Methylation; D017931:DNA Primers / Q000737:chemistry; D005260:Female; D015894:Genome, Human; D051549:Glutathione S-Transferase pi / Q000235:genetics; D006801:Humans; D009691:Nucleic Acid Denaturation; D016133:Polymerase Chain Reaction / Q000379:methods*; D013447:Sulfites / Q000737:chemistry*; D013696:Temperature
D019313:BRCA1 Protein; C492913:BRCA1 protein, human; D017931:DNA Primers; D013447:Sulfites; D004247:DNA; C496556:GSTP1 protein, human; D051549:Glutathione S-Transferase pi; C042345:hydrogen sulfite