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Triplex Oligos Enable Targeted DNA Methylation

July 8, 2010 There’s a new tool out there, and it’s made for all of those researchers out there who have ever pointed to a bit of genomic sequence and wondered, “what would happen if that promoter CpG was methylated right there?”

A new technique detailed in the latest issue of Bioconjugate Chemistry can help answer questions like that by targeting DNA methylation directly to the genomic sites you want. The trick is to fuse a triple helix forming oligonucleotide (TFO), used for targeting, to a reduced activity variant of the methyltransferase M. SssI, which methylates the target site.

The development team from the University of Groningen, Synvolux Therapeutics (Netherlands), RWTH Aachen University (Germany) and the Hungarian Academy of Sciences, tested out their new creation by targeting a specific site in the epithelial cell adhesion molecule (EpCAM) promoter in order to silence that gene. Although reduced EpCAM expression was not seen, probably because the CpG chosen wasn’t critical to promoter activity, they were able to demonstrate specific targeting and methylation of the intended site, proving that their technique worked.

The authors point out that their method has several slick features:

• TFO targeting domain gives the flexibility to target any genomic site
• M. SssI variant (2-5% of WT activity) prevents background methylation
• TFOs are cheaper and easier to synthesize than alternatives like Zinc Finger Proteins (ZFPs)
• Potential to permanently silence genes by altering promoter methylation rather than transiently affecting mRNAs

All of that makes it possible to find the individual CpGs crucial to activity in your favorite promoter, and creates a powerful tool for research or therapeutic uses. See if TFOs can hit the bullseye in your hands at Bioconjugate Chemistry, July 2010.