Disruption of Higher Order DNA Structures in Friedreich’s Ataxia (GAA)n Repeats by PNA or LNA Targeting

Helen Bergquist, Cristina S. J. Rocha, Rubén Álvarez-Asencio, Chi-Hung Nguyen, Mark. W. Rutland, C. I. Edvard Smith, Liam Good, Peter E. Nielsen, Rula Zain; PLoS ONE 11(11): e0165788. doi:10.1371/journal.pone.0165788

Chemical and structural probing of GAA repeats provides evidence for pyrimidine triplex (H-DNA) formation and the presence of different structures at the pathological repeats. Furthermore, we find that PNA and LNA sequence-specific targeting of Friedreich’s ataxia GAA repeat expansions can alter and resolve higher order DNA structures. BQQ-OP mediated triplex-specific cleavage of double strand DNA and chloroacetaldehyde chemical modification of single strand DNA regions at (GAA)n repeats demonstrate that GAA-PNA binding result in a duplex invasion complex, that completely dissociates all detectable triplex containing higher order structures at this site, whereas this is not the case for CTT-PNA. Additionally, we obtained a similar pattern using LNA based ONs. Furthermore, a significant change in plasmid morphology in the presence of GAA-LNA was detected using atomic force microscopy. Our results suggest that DNA targeting by modified GAA-oligomers at expanded (GAA)n repeats can be employed to examine the possible role of non-canonical DNA structures in FXN gene silencing and potentially applied to develop new nucleic acids-based therapeutic strategies in Friedreich’s ataxia disease.

 Disruption of Higher Order DNA Structures in Friedreich’s Ataxia (GAA)n Repeats by PNA or LNA Targeting