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.
Schematic of some the main parallel and anti-parallel G-quadruplexes investigated. Top panel shows the overall structure, with blue (red) indicating the G (C) bases, respectively. The middle panel gives the structure of specific G-quartets within quadruplexes (note that these alternate for the antiparallel structures). Finally, bottom panels give final conformations after extensive molecular dynamics simulations of corresponding DNA and RNA structures (side and top view) with green balls indicating ion locations.
Prof. Roland received his Ph.D. in 1989 from McGill University where he worked on theoretical aspects of the kinetics of first order phase transitions. He subsequently spent one year as a postdoctoral fellow at the University of Toronto before moving onto AT&T Bell Laboratories, where his work focused on understanding epitaxial growth on silicon surfaces. He joined the Department of Physics, North Carolina State University in 1993, and has been there ever since. At NC State, his work continued to focus on semiconductor growth problems, properties of carbon nanotubes, and quantum transport through molecular devices.
Over the past decade, his research has transitioned into the area of biomolecular simulations and he has worked on free energy methods, glycopeptide antibiotics, polyproline and polyglutamine peptides, and – most recently – the atypical DNA and RNA structures associated with neurodegenerative repeat diseases. Prof. Roland is a Fellow of the American Physical Society.
Prof. Sagui received her Licentiate degree from the University of San Luis, Argentina. She then moved to the University of Toronto for her doctorate which she received in 1995 for her work on the kinetics of phase separation in systems with short-range attractive and long-range repulsive interactions. She spent two years at McGill University where she continued her investigations of phase separating systems before moving onto the National Institute of Health and Environmental Sciences (NIEHS) in North Carolina with a Sloan Postdoctoral Fellowship award. There, her work focused on developing algorithms for simulating the delicate long-range electrostatic interactions, which are a crucial ingredient of all atomistic biomolecular simulations. In particular, she developed efficient algorithms for the treatment of permanent and induced multipolar interactions, as well as an O(N) multigrid method. She also helped develop the Adaptively Biased Molecular Dynamics (ABMD) method for the calculation of biomolecular free energies.
In recent years, Prof. Sagui’s work has focused on disordered peptides and fibril formation in amyloid and prion peptides. At present, she is working on nucleic acid structures, especially those associated with neurodegenerative trinucleotide and hexanucleotide repeat diseases. Prof. Sagui is a co-author of the AMBER simulation package and a Fellow of the American Physical Society.
Dr. Yuan Zhang
Dr. Yuan Zhang received her B.S. in Physics in 2009 from the University of Science and Technology of China, where she worked on the theoretical study of electronic structure of graphene. She received her Ph.D. in 2016 from the Department of Physics at North Carolina State University under the supervision of Prof. Celeste Sagui and Prof. Christopher Roland. Her thesis focused on the structural and dynamic characterization of various proteins and nucleotides associated with neurodegenerative diseases by using all-atom molecular dynamics. She continued to work with at NC State as a postdoctoral scholar for a year when she performed an extensive in silico investigation of the structure and dynamics of DNA and RNA G-quadruplex structure that can be formed from the GGGGCC and TGGGCC hexanucleotide repeat, which is the work highlighted here.
In 2017, Dr. Zhang joined Prof. Jinfeng Zhang’s group in the Department of Statistics at Florida State University as a postdoctoral scholar. Her current research focuses on protein surface recognition and comparison, which can be used for biomolecular identification and readily extended to address the protein identification problem in CET experiments. She also develops models with deep learning neural networks for protein design problems.
Zhang, Y., Roland, C., and Sagui, C. Structural and Dynamical Characterization of DNA and RNA Quadruplexes Obtained from the GGGGCC and GGGCCT Hexanucleotide Repeats Associated with C9FTD/ALS and SCA36 Diseases, ASC Chemical Neuroscience 9 (2018) 1104-1117