FIG. 2.

In vivo DMS footprinting of the M-MuLV 5′ LTR in fibroblasts. An autoradiogram from gel electrophoresis of labeled LMPCR products obtained from M-MuLV-infected 43-D fibroblasts is shown. The autoradiogram is representative of multiple analyses with the same nested oligonucleotide primer set. The portion of the gel shown corresponds to nucleotides −182 to −343 in the upstream M-MuLV LTR. The relative positions of previously characterized nuclear protein binding sites are indicated on the left. Both 75-bp direct repeats of the M-MuLV enhancer are displayed, and the region of interest is expanded at the right. The boxed sequences at the far right correspond to the NF-1, LVb, and Core sites. Comparisons between the in vitro-DMS-treated DNA control in the lane to the left and the in vivo-DMS-treated sample in the lane to the right indicated protection of certain guanine bases and hypersensitivity of other guanine bases in the infected cells. Guanine-specific protection is indicated by arrows pointing away from bands, and guanine or adenine hypersensitivity to DMS is indicated by arrows pointing towards the bands. Other investigators have previously reported hypersensitivity of adenines in in vivo DMS-LMPCR footprinting. The lengths of the arrows indicate the relative magnitudes of the protection or hypersensitivity.