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Adding my two cents to the other suggestions: Boehringer Mannheim (among
others) make a fluorescein labelled dUTP. This can be incorporated into
DNA using PCR by adding it to the PCR mix (they sell a kit for this).
You didn't mention where the DNA came from or whether or not you had
constructed it yourselves. But if PCR can be used then you can label
the DNA this way and transfect it into cells because it behaves more or
less like normal DNA. I don't know if this would be sensitive enough
though. Depends on the tranfection effeciency (which is often low).
Another idea is to transfect your cells with the DNA of interest, fix
them, permeabilize them and use fluorescent in situ PCR (with dUTP for
example) to identify cells containing the sequence of interest. This
assumes that you have PCR primers for your sequence (and thus knowledge
of the sequence) and that you won't need live cells afterwards. The
advantage is extreme sensitivity. Have a look at Patterson et al
Science 1993 260:976-9 for an informative example (the paper is about
RNA detection but its the same basically without the reverse
transcriptase step).
AL
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