dsRNA stain?

[Chris Wood-5]

Dear List,

A collaborator wishes to follow virus entry and processing in live cells in real
time, and wants to label both the dsRNA genome of the virus and its outer
capsid with separate fluorophores to be able to follow them both after entry.
He's already decided on quantum dots for the capsid labelling (they tried xFPs
but they interfered with capsid packing) but came to me asking for advice for a
nucleic acid stain. His idea would be to culture the virus in its usual host cells
and label the genome during synthesis/shedding of the virus, isolate the
labelled titer and then follow virus component fate after infection in the target
cells.

I have plenty of experience in DNA staining of nuclei, but none with staining
RNA (apart from cursing it as a source of background). Are any particular dyes
more suitable for staining dsRNA than others? One concern would be to have
sufficiently high relative affinity for RNA over DNA, to maximize labelling during
virus harvesting over nuclear labelling of the host cells, and to reduce transfer
from the labelled virus to the target cell nucleus during infection.

All help and advice most gratefully received,

Chris Wood
Instituto de Biotecnología
Universidad Nacional Autónoma de México

[qiqi_1983]

Hello Chris,
You can check "SYTO RNA selective" from Invitrogen. I'm planning to use it.