Duplexes Formed by G₄C₂ Repeats Contain Alternate Slow- and Fast-Flipping G·G Base Pairs

Aberrant expansion of the hexanucleotide GGGGCC (or G₄C₂) repeat in the human C9ORF72 gene is the most common genetic factor found behind amyotrophic lateral sclerosis and frontotemporal dementia. The hypothesized pathways, through which the repeat expansions contribute to the pathology, involve one or more secondary structural forms of the DNA and/or RNA sequences, such as G-quadruplexes, duplexes, and hairpins. Here, we study the structures of DNA and RNA duplexes formed by G₄C₂ repeats, which contain G(syn)·G(anti) base pairs flanked by either G·C or C·G base pairs. We show that duplexes formed by G₄C₂ repeats contain alternately two types of G·G pair contexts exhibiting different syn-anti base flipping dynamics (∼100 ms vs ∼2 ms for DNA and ∼50 ms vs ∼20 ms for RNA at 10 °C, respectively) depending on the flanking bases, with the slow-flipping G·G pairs being flanked by a guanine at the 5'-end and the fast-flipping G·G pairs being flanked by a cytosine at the 5'-end. Our findings on the structures and dynamics of G·G base pairs in DNA and RNA duplexes formed by G₄C₂ repeats provide a foundation for further studies of the functions and targeting of such biologically relevant motifs.