Structure-Specific Recognition of Friedreich's Ataxia (GAA)n Repeats by Benzoquinoquinoxaline Derivatives

Expansion of GAA triplet repeats in intron 1 of the FXN gene reduces frataxin expression and causes Friedreich's ataxia. (GAA)(n) repeats form non-B-DNA structures, including triple helix H DNA and higher order structures (sticky DNA). In the proposed mechanisms of frataxin gene silencing, central tranfered questions involve the characterization of non-B- DNA structure(s) that are strongly suggested to play a role in fratax in expression. Here we examined (GAA)(n) binding by triplex-stabilizing benzoquinoquinoxaline (BQQ) and the corresponding triplex DNA cleaving BQQ-1, 10 phenanthroline (BQQ-OP) compound. We also examined the ability of these compounds to act as structural probes for H-DNA formation within higher order structures at pathological frataxin sequences in plasmids DNA complex formation analyses with a gel-mobility-shift assay and sequence-specific probing of H-DNA forming (GAA)(n) sequences by single strand oligonucleotides and triplex directed cleavage demonstrated that a parallel pyrimidine (rather than purine) triplex is the more stable motif formed at (GAA) repeats under physiologically relevant conditions.