Detection of RNA:DNA hybrid in E.coli

[rjstaunt]

Hi all (first post, new member)

I am trying to extract the gDNA from single cells of e.coli, but upon lysis the chromosome comes out yet remains tethered to the cell wall and does not free up or release, even when applying strong electrophoretic force. We believe a protein anchors an RNA to the peptidoglycan layer, and that the RNA hybridizes to the chromosome somewhere...

I am going to use RNase H and see if this works to free up the gDNA, but I want to verify the successful cleavage of the RNA-DNA bond.

Is there a chromophore out there that targets such hybrids?

Has anyone out there tried to detect RNA-DNA hybrids in vivo?

I have seen some articles by folks using FRET for this, but I've never tried that yet

Thank you all in advance,

Rory