Conditioning Wildflower Seed

Cooperative Bending of the 21-Base-Pair Repeats of the SV40 Viral Early Promoter by Human Sp1

“…The proposal that triple-helix-induced repression involves changes in DNA flexibility is in accord with the ideas presented here, namely, that DNA flexibility and bending are important components of the transcriptional regulation in the early promoter region of SV40 DNA. Last, the model proposed here has probable implications for other multi-zinc-finger binding proteins, such as TFIIIA (Churchill et al, 1990), in their protein-DNA complexes.…”

“…The hydroxyl-radical footprinting method provides a valuable means to examine the interaction of a DNA binding protein with the backbone of DNA, since hydroxyl radicals are small enough to cause strand breakage in DNA, even when complexed with DNA binding proteins or small DNA interactive ligands (Shafer et al, 1989;Burkhoff & Tullius, 1988). However, a direct interaction of the protein with DNA molecules through a minor groove site or severe changes in the DNA backbone conformation, such as bending in toward the minor groove, are also expected to cause significant reductions in the magnitude of hydroxyl-radical cleavage (Churchill et al, 1990;Yang & Nash, 1989). concentration of (+)-CC-1065 as that used in lane 8 was added to samples that also contained amounts of Spl equivalent to those used in the samples in lanes 2-4.…”

“…The diminished cleavage of the region between each GC box (see Figure 2) reveals an important structural aspect of the Sp 1 2 1 -bp repeat complex. Generally, diminished hydroxyl-radical cleavage of the DNA backbone can be attributed to either close contacts between the sugar phosphate backbone and DNA binding ligand (e.g., small molecules or DNA binding proteins) or a structural change in minor groove geometry (Burkhoff & Tullius, 1988;Churchill et al, 1990). DNA bending, which results in diminished hydroxyl-radical cleavage as a consequence of compression of the minor groove (Shafer et al, 1989;Burkhoff & Tullius, 1988;Churchill et al, 1990), is the most well-characterized structural change in minor groove geometry.…”

“…Generally, diminished hydroxyl-radical cleavage of the DNA backbone can be attributed to either close contacts between the sugar phosphate backbone and DNA binding ligand (e.g., small molecules or DNA binding proteins) or a structural change in minor groove geometry (Burkhoff & Tullius, 1988;Churchill et al, 1990). DNA bending, which results in diminished hydroxyl-radical cleavage as a consequence of compression of the minor groove (Shafer et al, 1989;Burkhoff & Tullius, 1988;Churchill et al, 1990), is the most well-characterized structural change in minor groove geometry. Suspicion that the correct explanation involves bending of DNA rather than steric occlusion for the diminished hydroxyl-radical cleavage stems from the observation that both 5'-AGTTA sequences located between GC boxes I11 and IV and V and VI show relatively diminished cleavage compared to the other regions (seepanelain Figure2C DNA in which this sequence has been replaced by a GC sequence that eliminates this intrinsically bent DNA structure.…”

“…However, it is not clear why Spl binding sites are arranged in the manner that Spl binds once every 10-12 bp, which roughly corresponds to one complete turn of the DNA helix. This situation is similar to the TFIIIA DNA complex, where zinc fingers bind in successive major grooves of DNA in a periodic manner (Churchill et al, 1990). In this study, we have addressed the question of the significance of the periodicity of Spl binding alongside the significance of sequences located between Spl binding sites.…”