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In order to exclude the possibility that AP-2α is affecting DNA methylation at the global level, an methylation sensitive digest was performed on DNAs from SCC22B cells with and without AP-2α downregulation.
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A selective methylation-sensitive digest enabled the low-levels of hypermethylated RASSF1 fetal DNA 34) to be accurately quantified using our ddPCR system.
The methylation status of the oligonucleotide was confirmed by CpG methylation sensitive restriction digest with AatII.
In the methylation-sensitive digest, premutations are detected as fragments of 2.9 to about 3.3 kb in males and on the active X chromosome in females, whereas 5.3 5.7 kb fragments correspond to the premutation on the inactive X chromosome.
For methylation-sensitive restriction digest, DNA was digested with BglII and HhaI (New England Biolab).
Initial studies using methylation-sensitive restriction enzyme digest techniques demonstrated that methylation at the promoter region and exon 1 of RB1 gene is associated with reduced levels of RB1 transcript (Greger et al, 1994).
Methylation status can be concluded based on the presence or absence of a PCR product in the methylation sensitive HpaII digest.
Alternatively, we used a methylation sensitive restriction enzyme to digest the rose genomic DNA, and low marker coverage would be expected in repetitive regions containing methylated residues which is seen in other plant species42.
Amplification of the MSP amplicon from the Hpa II-digested DNA occurs only when the DNA is methylated at the -96 CpG as Hpa II is methylation sensitive and will only digest unmethylated but not methylated DNA.
Restriction enzyme-based methods exploit the property of methylation-sensitive enzymes which only digest unmethylated DNA and methylation-dependent enzymes which only cut methylated DNA.
If a significant fraction of sensitive cells were digested beyond recognition in the microscope, they would be missed in this fluorescence assay and the calculated survival would represent an overestimate of the true rate of cell survival.
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