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 Binding Factor (NssBF), located in the long terminal repeat of the Drosophila 1731 retrotransposon, was investigated by melting temperature experiments, chemical probing and fluorescence measurements using a macrocyclic bis-acridine. The most probable structure of this element, named Bc, mainly involves two hairpins in equilibrium at pH 6.0 at low concentration. The hairpins differ in their apical loop size; 4 and 8 nt. The structural flexibility of Bc probably derives from the three consecutive CATA repeats complementary to the GTAT nucleotides of the palindrome. In contrast, the Bc complementary strand adopts a single hairpin. Since Bc is implicated in repression of transcription via binding of two specific factors, its structural flexibility could be associated with this process.
Slama-Schwok
A
A
INSERM U310, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France. schwok@ibpc.fr
Brossalina
E
E
Demchenko
Y
Y
Best-Belpomme
M
M
Vlassov
V
V
D000166:Acridines; D000818:Animals; D001483:Base Sequence; D004247:DNA / Q000737:chemistry* / Q000235:genetics*; D004330:Drosophila / Q000235:genetics*; D005456:Fluorescent Dyes; D006863:Hydrogen-Ion Concentration; D009690:Nucleic Acid Conformation; D015345:Oligonucleotide Probes / Q000235:genetics; D018626:Retroelements / Q000235:genetics*; D020079:Terminal Repeat Sequences; D013816:Thermodynamics
D000166:Acridines; D005456:Fluorescent Dyes; D015345:Oligonucleotide Probes; D018626:Retroelements; C106828:macrocyclic bis-acridine; D004247:DNA