The parallel tetrameric DNA G-quadruplex formed by the two-repeat C9orf72 GGGGCC sequence in solution

The abnormal expansion of G-rich hexanucleotide repeat, GGGGCC (G4C2), in chromosome 9 open reading frame 72 (C9orf72) is known to be the prevailing genetic cause of two fatal degenerative neurological diseases, amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). It is well known that the DNA G4C2 repeat expansion with different lengths can form G-quadruplexes which affect gene transcription related to ALS/FTD, therefore it is crucial to understand DNA G4C2 G-quadruplex structures. Herein, by utilizing nuclear magnetic resonance (NMR) spectroscopy, we examined DNA G-quadruplex structure adopted by two G4C2 hexanucleotide repeats with an inosine substitution at position 4, d(G4C2)₂-I4. We show that d(G4C2)₂-I4 folds into an eight-layer parallel tetrameric G-quadruplex containing two parallel dimeric G-quadruplexes stacking together through π-π interaction via 5′-to-5′ mode in solution. Each dimeric G-quadruplex unit involves two propeller loops composed of two cytosine bases. This result is consistent with the observation in the crystal structure of d(G4C2)₂. Our work not only sheds light on the structural diversity of G-quadruplexes adopted by d(G4C2)_n but also provides a structural basis for drug design in treatment of ALS and FTD.