The overall structural features of the multimeric complex between Spl and the 21-base-pair repeat of the early promoter region of SV40 DNA have been determined using hydroxyl-radical footprinting; (+)-CC-l 065, a sequence-specific minor groove bending probe; and circularization experiments. The results show that the 21-base-pair repeat region has an intrinsically in-phase bent structure that is stabilized upon saturation Sp1 binding by protein-DNA and protein-protein interactions to produce a looping structure. The direction of the Sp1-stabilized bending of DNA occurs into the minor groove and is localized between each of the Sp1 binding sites. These results are used as the basis to propose a looping structure for the multimeric Sp1 21-base-pair repeat region of SV40 DNA. Last, these results provide a rationale for the recently observed inhibition of basal transcriptional levels by site-specific triple-helical DNA complexes.
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