A eukaryotic alternating purine and pyrimidine sequence forms an altered structure similar to Z-DNA

A domain rich in alternating purines and pyrimidines (Pu/Py) from RU, a cloned repeat unit of the complex (G+C)-rich satellite DNA of the Bermuda land crab, has been subcloned into the Clal site of pBR322 to construct hybrid plasmid pZEl5-4.53kb. A smaller plasmid, pZEl5-2.66kb, was derived from pZE15-4.53kb by deletion of a 1881 bp segment between the EcoRV and PvuII sites followed by recircularization with BamHI linkers. The domain consists of a 53 bp stretch rich in Pu/Py with the potential to form Z-DNA, which may be represented as Z₆N₃Z₉Z₄Z₅NZ₁₅NZ₅Z₄, where Z = Pu/Py and N = interruptions in E>u/Py. Included in the domain is a 35 bp segment (Z₄Z₅NZ₁₅NZ₅Z₄) most of which is highly conserved. However, in at least two other copies, 10 and 12 bp deletions have been observed in the Z₆ and Z₉ segments (Fowler et al., 1985; Stringfellow et al., 1985b). As evidenced by inhibition of BssHII cleavage, binding of anti-Z-DNA antibodies to supercoiled plasmids coupled with identification of the restriction fragments containing the binding sites, and cleavage of B-Z junctions with SI nuclease, the domain adopts an altered conformation with properties similar to those of Z-DNA. The specific arrangement of Pu/Py in the crab satellite might allow the Z₄Z₅NZ₁₅NZ₅Z₄ segment to adopt, at least transiently, a Z-DNA structure with dyad symmetry along the phosphodiester backbone. It is hypothesized that this structure could serve as a binding site for proteins.