Detection of Proteins Binding to Short RNA.DNA Hybrids or Short Antisense Oligonucleotides in Xenopus laevis Oocytes and Human Macrophage Cell Extracts by Photoaffinity Radiolabeling

Using a 12 base pair RNA.DNA hybrid, substituted with bromouracil on either the RNA or DNA strand, we have detected by photoaffinity radiolabeling a limited set of proteins able to bind to RNA.DNA hybrids in both Xenopus oocyte extracts and human macrophage extracts. Resulting patterns of crosslinked proteins were highly dependent on the strand (DNA or RNA) that was substituted. With one exception, none of the proteins investigated in competition experiments was found to be absolutely specific for RNA.DNA hybrids, as at least one other nucleic acid, either single-stranded DNA or single -stranded RNA, was found to compete efficiently. None of the proteins detected in this assay correspond to the size expected for RNases H. Using the same methodology, we have detected proteins that bind to short oligodeoxyribonucleotides. Although we have essentially detected in Xenopus oocytes one prominent protein of ≈ 75 kDa, corresponding to replication protein A (RPA) whatever the oligonucleotide used, the patterns obt...