G-quadruplex structure of G/C-rich Hexanucleotide repeats

The mutational expansion of hexanucleotide repeats (HRs) is responsible for different hereditary neurodegenerative disorders in humans. Some of the neurological disorders associated with the expansion of HRs include frontotemporal dementia (C9FTD), amyotrophic lateral sclerosis (ALS) and spinocerebellar ataxia 36 (SCA36). The GGGGCC hexanucleotide repeat (HR) expansion within the first intron of the C9ORF72 gene causes frontotemporal dementia (C9FTD) and amyotrophic lateral sclerosis (ALS) while GGGCCT HR expansion within intron 1 of the NOP56 gene on chromosome 20 causes spinocerebellar ataxia 36 (SCA36). Although the severity of C9FTD and ALS increases with the length of the HRs, the severity of SCA36 does not seem to vary with the length of the HRs. Nonetheless, both GGGCCC and GGGCCT HRs tend to form stable G-quadruplex structures, which is a common causative factor for expansion in human disease. Despite the establishment of a clear connection between the aforementioned human neurodegenerative diseases and the associated secondary structures, there is a dearth of information on the structural and dynamic characteristics of the G-rich quadruplexes that are specifically associated with the GGGGCC and GGGCCT HRs. Furthermore, the techniques used to study the structure of these HRs lack detailed molecular resolution.

Thus, North Carolina State University scientists: Yuan Zhang (Postdoctoral Fellow), Profs. Celeste Sagui and Christopher Roland, from the Department of Physics used molecular dynamics microsecond simulations to obtain a structural and dynamical characterization of the DNA and RNA quadruplexes obtained from the GGGGCC and GGGCCT HRs associated with C9FTD/ALS and SCA36 diseases. The research work is published in the journal, ASC Chemical Neuroscience.

The authors observed that both parallel and antiparallel DNA G-quadruplexes are stable, with or without stabilizing loops while the presence of loops confers more stability to RNA G-quadruplexes. However, only parallel and one antiparallel RNA G-quadruplexes were stabilized by the presence of loops. They also discovered that as the RNA bases recovered their preferred sugar conformation of C3′-endo, the C2′-endo sugars which maintained the initial RNA antiparallel quadruplexes transitioned to C3′-endo sugars. This triggered the unwinding and buckling of the flat G-tetrads, as well as the unfolding of the RNA antiparallel quadruplex.

Moreover, the research team from the North Carolina State University observed that parallel G-quadruplexes stabilize the adjacent C-tetrad bases into a quartet in both DNA and RNA. The C-tetrad is stabilized by cyclical hydrogen bonds, molecular interactions with the preceding G-tetrad and the presence of ions between the C-tetrad and G-tetrad. In addition, the flat C-layers at the ends of the quadruplexes are stabilized by antiparallel DNA G-quadruplexes. Furthermore, the authors observed that quadruplex stabilization by potassium ions are better than quadruplex stabilization by sodium ions.

Yuan Zhang and colleagues’ study provide compelling evidence on the structural polymorphism at both DNA and RNA levels obtained from the GGGGCC and GGGCCT HRs associated with C9FTD/ALS and SCA36 diseases. These findings will advance further studies on the atypical secondary structures of HRs at the atomic level and facilitate the development of a mechanistic model for the simulation of neurodegenerative disorders caused by the mutational expansion of simple sequence repeats in the human genome.