A long polypyrimidine:polypurine sequence in 5' flanking region of arylsulfatase gene of sea urchin embryo.

Sea urchin (Hemicentrotus pulcherrimus) arylsulfatase(Ars) gene contains a long (622 bp) polypyrimidine:polypurine (Pyr-Pur) sequence in its 5' flanking region. The Pyr-Pur sequence inserted into a plasmid was sensitive to S1 nuclease at a low acidic pH (pH 5) when the plasmid was negatively supercoiled. From the distribution pattern of S1 sites in the Pyr-Pur region it is concluded that a (CT)11:(GA)11 tract in this region could adopt an unusual DNA configuration distinct from the usual B-form. Another feature of the Pyr-Pur sequence is that this (CT)11:(GA)11 tract is sandwiched by two oligo(dC):oligo(dG) stretches (G-strings) that are located at almost an equal distance from both ends of the (CT)11:(GA)11 tract. Mobility shift assay and DNase-I footprinting revealed that the gastrula nuclei contain nuclear proteins that interact with two distinct oligo(dG):oligo(dG) tracts (G-strings) in the Pyr-Pur region. The possibility is suggested that G-strings may be related to formation and stabilization of an unusual DNA configuration of a (CT)11:(GA)11 tract.