Possible structures of homopurine-homopyrimidine S1-hypersensitive sites

S1 nuclease hypersensitive sites in the 5' flanking regions of eukaryotic genes, present in small artificial supercoiled DNA circles, reside in homopurine-homopyrimidine stretches. The hierarchical behavior which these sites exhibit is consistent with the notion that they act as sinks of torsional free energy. By employing DMS as a single-strand-specific reagent, we show that these sites (despite their S1 sensitivity) are regions of duplex DNA. A simple thermodynamic treatment indicates that the high torsional stress in the small DNA circles is almost certain to be relieved by the formation of alternate DNA structures. The same treatment places some constraints on the types and sizes of the regions with alternate conformation. While no definitive structural conclusions can be drawn, left-handed helices seem most consistent with the extent and the pattern of sensitivity to S1 nuclease.