NMR structure of a G-quadruplex formed by four d(G4C2) repeats: insights into structural polymorphism

Nucleic Acids Res. 2018 Nov 30;46(21):11605-11617. doi: 10.1093/nar/gky886.

Abstract

Most frequent genetic cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), is a largely increased number of d(G4C2)n•(G2C4)n 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. Oligonucleotide d[(G4C2)3G4], which represents the shortest oligonucleotide model of d(G4C2) repeats with the ability to form a unimolecular G-quadruplex, forms two major G-quadruplex structures in addition to several minor species which coexist in solution with K+ ions. Herein, we used solution-state NMR to determine the high-resolution structure of one of the major G-quadruplex species adopted by d[(G4C2)3G4]. Structural characterization of the G-quadruplex named AQU was facilitated by a single substitution of dG with 8Br-dG at position 21 and revealed an antiparallel fold composed of four G-quartets and three lateral C-C loops. The G-quadruplex exhibits high thermal stability and is favored kinetically and under slightly acidic conditions. An unusual structural element distinct from a C-quartet is observed in the structure. Two C•C base pairs are stacked on the nearby G-quartet and are involved in a dynamic equilibrium between symmetric N3-amino and carbonyl-amino geometries and protonated C+•C state.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Pairing
  • C9orf72 Protein / genetics*
  • Deoxyguanosine / analogs & derivatives
  • Deoxyguanosine / chemistry
  • G-Quadruplexes*
  • Guanine / chemistry
  • Humans
  • Magnetic Resonance Spectroscopy
  • Models, Molecular
  • Nucleic Acid Conformation
  • Polymorphism, Genetic
  • Repetitive Sequences, Nucleic Acid

Substances

  • 8-bromo-2'-deoxyguanosine
  • C9orf72 Protein
  • C9orf72 protein, human
  • Guanine
  • Deoxyguanosine