Mosaic divergent repeat interruptions of motif length and sequence, mDRILS, of XDP-linked repeats affect formation of DNA/RNA triplexes & quadruplexes

An inserted SINE-VNTR-Alu(AGAGGG)n repeat into the TAF1 gene is the cause of X-linked dystonia-parkinsonism. Mosaic divergent repeat interruptions affecting both motif length and sequence (mDRILS) of the canonical repeat (AGAGGG)n arise and can diminish repeat instability and delay disease age of onset. The repeat itself may affect gain-of-function disease pathways. Consequently, XDP etiology may involve unusual structures formed by the repeats. To study the effects of mDRILS on the formation of unusual structures of the XDP TAF1-SVA repeat, we designed a series of G-rich DNA and RNA oligonucleotides having the pure canonical repeat 5'-(AGAGGG)4-3', or either of the most common mDRILS 5'-(AGAGGG)2AGGG(AGAGGG)-3'; and 5'-(AGAGGG)2AGG(AGAGGG)-3'. Circular dichroism, thermal melting, binding of the G-quadruplex ligand TMPyP4, shows the first canonical and AGGG-interrupted sequence assume K+-sensitive stable G-quadruplexes, whereas GA duplexes are the prominent structure in the AGG-interrupted form. The complementary C-rich strands, 5'-(CCCTCT)4-3', and 5'-(CCCTCT)2CCCT(CCCTCT)-3', and 5'-(CCCTCT)2CCT(CCCTCT)-3', assumed i-motif-compatible structure. Mixtures of the G- and C-rich complementary sequences, at 1:2 ratios, showed triplex-forming propensity for the canonical and AGGG-interrupted, but not the AGG-interrupted forms. The ability of mDRILS to elicit modifications of the disease-causing XDP TAF1-SVA repeat to enable or disable the formation of specific structures, such as quadruplex and triplex structures, may explain in part how mDRILS mediate their disease-modifying effects.