In situ nucleoprotein structure at the SV40 major late promoter: melted and wrapped DNA flank the start site.

New in situ probing methods have been developed and used to probe the nucleoprotein structures at the SV40 major late promoter in infected monkey cells. The region that contains the three proximal transcription elements was probed with DNase I and micrococcal nuclease in transcriptionally active, permeabilized cells, and with the single-strand selective reagent KMnO4 in intact cells. The downstream element is included in a region of enhanced DNase I reactivity at 10- to 11-bp intervals for approximately 140 bp, presumably because of DNA wrapping around a specifically positioned nucleosome particle. The two other proximal DNA elements appear to be mostly melted, with a protecting factor bound primarily to the template DNA strand. The protecting factor directly borders the wrapped particle. These observations provide an initial description of parts of the biological transcription machinery and suggest that the SV40 major late promoter elements are part of a higher order nucleoprotein complex that involves wrapped and melted DNA.