STRUCTURAL FLEXIBILITY OF A DNA HAIRPIN LOCATED IN THE LONG TERMINAL REPEAT OF THE DROSOPHILA-1731 RETROTRANSPOSON

The structure of the DNA binding site of the Nuclear single-stranded B inding Factor (NssBF), located in the long terminal repeat of the Dros ophila 1731 retrotransposon, was investigated by melting temperature e xperiments, chemical probing and fluorescence measurements using a mac rocyclic bis-acridine, The most probable structure of this element, na med Be, mainly involves two hairpins in equilibrium at pH 6.0 at low c oncentration. The hairpins differ in their apical loop size; 4 and 8 n t, The structural flexibility of Be probably derives from the three co nsecutive CATA repeats complementary to the GTAT nucleotides of the pa lindrome. In contrast, the Be complementary strand adopts a single hai rpin. Since Be is implicated in repression of transcription via bindin g of two specific factors, its structural flexibility could be associa ted with this process.