in vitro transcription/ab-depletion

[hcavaco at fm.ul.pt]

I am trying to investigate whether a certain factor is affecting in- vitro
run-off transcription using adenoviral promotors. One important experiment
would be to immunodeplete the nuclear extract from HeLa cells using
antibodies bound to Protein-A-Sepharose. However, the first approach
revealed that non-specific transcription signals were increased while
production of specific transcripts as observed in the absence of
antibody-depletion was reduced. Identical results were obtained with the
specific  as well as a non-specific control serum. 
Does anyone have experience or useful suggestions and references on how to
optimize conditions for such experiments.
e-mail hpeter at fm.ul.pt