Properties of the nucleic acid needed to induce MHC expression in cells. Transfection and Northern analysis were performed exactly as described for Fig. 1. (a) FRTL-5 cells were transfected with intact, methylated, or DNase-treated plasmids, pcDNA3 or pRc/RSV (lanes 3–8), ss CpG ODNs or control ODNs (lanes 9–12), or ss or ds phosphorothioate oligonucleotides (s-oligos; lanes 13–16). Lane 1 contains RNA from nontreated cells, and lane 2 contains only RNA from cells subjected to the transfection procedure. ODN-1 is the Foamy virus oligonucleotide. ODN-2 is the cytomegalovirus oligonucleotide. CpG-1 is GCTAGACGTTAGCGT; non CpG-1 is GCTAGATGTTAGCGT; CpG-2 is TCAACGTTGA; and non CpG-2 is TCAAGCTTGA. (b) Various synthetic polynucleotides and their duplexes were transfected similarly and analyzed (lanes 3–16). (c) Cells were transfected with 5 μg of dsDNA fragments from 24 bp to 1,004 bp in length (lanes 3–10) or with the indicated amount of 25-bp dsODNs (lanes 12–15). MHC class II expression was measured 48 h later by reverse transcription–PCR (15, 16). Cells treated with 100 units/ml γIFN for 48 h were the positive control. These results are typical of at least five different experiments performed on different batches of cells.