Most frequent genetic cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), is a largely increased number of d(G4C2) repeats located in the non-coding region of C9orf72 gene. Non-canonical structures, including G-quadruplexes, formed within expanded repeats have been proposed to drive repeat expansion and pathogenesis of ALS and FTD. Within the study, the structure of G-quadruplex with atomic resolution, formed by the oligonucleotide with four repetitions of d(G4C2) was determined. G-quadruplex structure consist of four G-quartet planes, three lateral loop and two C•C base pairs stacked on the outer G-quartet. High resolution structure of the G-quadruplex determined here enables development of small molecules that could control the formation of the supposedly toxic G-quadruplex structures in the cells. The study also showed that the pH of the solution can control stability of G-quadruplex, which contributes to predicting of the folding and understanding of the structural diversity of oligonucleotides rich in guanine and cytosine.
Using global thermodynamic analysis of structural transitions of an AGCGA-repeat oligonucleotide, we show why it populates certain states at given temperatures. We suggest that AGCGA-quadruplex folding is, similarly to folding of B-DNA, stabilized by hydrophobic desolvation accompanied by specific binding of water molecules to polar pockets. In contrast to B-DNA, it appears that H-bonding and base-stacking stabilize AGCGA-quadruplex structure to an extent that still enables substantial conformational flexibility. Therefore, we believe that this work represents an important step in elucidating thermodynamic principles by which AGCGA-rich sequences fold into specific tetrahelical structures.