Duplex Destabilization in Superhelical DNA is Predicted to Occur at Specific Transcriptional Regulatory Regions

Abstract

Analytic methods that accurately calculate the extent of duplex destabilization induced in each base-pair of a DNA molecule by superhelical stresses are used to analyze several genomic DNA sequences. Sites predicted to be susceptible to stress-induced duplex destabilization (SIDD) are found to be closely associated with specific transcriptional regulatory regions. Operators within the promoters of SOS-regulated Escherichia coligenes are destabilized by superhelical stresses, whereas closely related sequences present elsewhere on that genome are not. Analysis of genomic sequences from the budding yeast Saccharomyces cerevisiaefinds a distinctive tripartite pattern, in which the 3′ and 5′ termini of genes are destabilized, but the sequence encoding the primary transcript is not. Three rDNA genes from higher eukaryotes exhibit a similar pattern. Implications of these results regarding possible mechanisms of activity of the regions involved are discussed. A strategy is presented for designing experiments in which the susceptibility to SIDD of a local region is altered without changing its local base sequence. The occurrence of the observed SIDD patterns provides a new approach to searching uncharacterized genomic sequences for transcriptionally active regions.