Plasticity of DNA conformation around the Drosophila melanogaster alcohol dehydrogenase gene under torsional stress.

ABSTRACT

Genomic DNA of eukaryotes is thought to be organized into multiple topological domains whose conformation can be independently regulated by torsional stress. We have demonstrated the formation of altered DNA structures around the Drosophila melanogaster alcohol dehydrogenase (Adh) gene by sensitivity to endonucleases and by binding single-strand binding (SSB) protein. Several altered DNA structures were detected only on torsionally stressed DNA at specific sites. Some corresponded to the two initiation cap sites and the poly(A) addition sites and others were found in the 5'-flanking regions of both the adult and larval cap sites and in the 3'-flanking region of the Adh gene. In particular, the 5'-flanking regions both exhibited a plasticity of DNA conformation according to the strength of torsional stress and the concentration of Mg2+. SSB protein bound preferentially to the non-coding regions of the Adh gene only on torsionally stressed DNA and not on relaxed or linear DNA. The observed binding preference appeared to correspond to the thermodynamic stability of the base-pairs involved. These results suggest that DNA conformation is specifically organized around the Adh gene for gene function. The plasticity of DNA may play a role in the regulation of transcriptional activation.