A NOVEL UNUSUAL DNA-STRUCTURE FORMED IN AN INVERTED REPEAT SEQUENCE

A potential to form a non-cruciform unusual DNA structure was shown at the inverted repeat DNA sequence of a fish satellite DNA. The recombi nant plasmid harbouring a member of the EcoRI satellite family of Sill ago japonica (Percoidei, Sillaginidae) was subjected to S1 nuclease tr eatment, and the cutting sites were mapped by primer extension assay. The S1 nuclease attacked the 3'-half of the inverted repeat but not th e middle part of symmetry under various salt conditions, suggesting th at this unusual DNA structure is different from the DNA cruciform and a conventional intramolecular tripler structure. In the presence of 20 0 mM potassium chloride, the typical DNA cruciform has extruded, sugge sting that certain purine-purine-pyrimidine base triads are involved i n the formation of this unusual DNA structure. These results support t he occurrence of a novel unusual DNA structure formed in the inverted repeat sequence. (C) 1998 Academic Press.