I only have this enzyme in the lab to promote in vitro transcription. I know I should get another DNA template subcloned with a SP6 promoter, however I am very curious to know if SP6 RNA polymerase would work in such very related promoter (T7).
I know from bitter experience that these two RNA polymerases only recognize their own promoter and are not interchangeable. Sorry but you need to reclone or change your enzyme.
I think the SP6 polymerase will not start from a T7 promoter. We use vectors with both promoters for generation of antisense and sense probes and get the specific products only. Nevertheless it might be a different situation if only the unspecific promoter is present but the amount of RNA will be rather low. I would subclone the insert.
I know from bitter experience that these two RNA polymerases only recognize their own promoter and are not interchangeable. Sorry but you need to reclone or change your enzyme.