Summary information [schematics · tetrads · helices · stems · costacks · homepage]

PDB-id
5oph
Class
DNA
Method
NMR
Summary
G-quadruplex structure of DNA oligonucleotide containing ggggcc repeats linked to als and ftd
Reference
Brcic, J., Plavec, J.: (2018) "NMR structure of a G-quadruplex formed by four d(G4C2) repeats: insights into structural polymorphism." Nucleic Acids Res., 46, 11605-11617.
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.
G4 notes
4 G-tetrads, 1 G4 helix, 1 G4 stem · 4(-Lw-Ln-Lw), chair(2+2), UDUD

Base-block schematics in six views [summary · tetrads · helices · stems · costacks · homepage]

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List of 4 G-tetrads [summary · schematics · helices · stems · costacks · homepage]

 1 glyco-bond=s-s- groove=wnwn planarity=0.279 type=bowl   nts=4 GGGG A.DG1,A.DG10,A.DG13,A.DG22
 2 glyco-bond=-s-s groove=wnwn planarity=0.178 type=other  nts=4 GGGg A.DG2,A.DG9,A.DG14,A.BGM21
 3 glyco-bond=s-s- groove=wnwn planarity=0.176 type=other  nts=4 GGGG A.DG3,A.DG8,A.DG15,A.DG20
 4 glyco-bond=-s-s groove=wnwn planarity=0.292 type=other  nts=4 GGGG A.DG4,A.DG7,A.DG16,A.DG19

List of 1 G4-helix [summary · schematics · tetrads · stems · costacks · homepage]

In DSSR, a G4-helix is defined by stacking interactions of G-tetrads, regardless of backbone connectivity, and may contain more than one G4-stem.

Helix#1, 4 G-tetrad layers, INTRA-molecular, with 1 stem

 1  glyco-bond=s-s- groove=wnwn Major-->WC nts=4 GGGG A.DG1,A.DG10,A.DG13,A.DG22
 2  glyco-bond=-s-s groove=wnwn WC-->Major nts=4 GGGg A.DG2,A.DG9,A.DG14,A.BGM21
 3  glyco-bond=s-s- groove=wnwn Major-->WC nts=4 GGGG A.DG3,A.DG8,A.DG15,A.DG20
 4  glyco-bond=-s-s groove=wnwn WC-->Major nts=4 GGGG A.DG4,A.DG7,A.DG16,A.DG19
  step#1  mm(<>,outward)  area=16.18 rise=3.43 twist=19.5
  step#2  pp(><,inward)   area=15.26 rise=3.49 twist=35.9
  step#3  mm(<>,outward)  area=16.48 rise=3.39 twist=17.8
  strand#1 DNA glyco-bond=s-s- nts=4 GGGG A.DG1,A.DG2,A.DG3,A.DG4
  strand#2 DNA glyco-bond=-s-s nts=4 GGGG A.DG10,A.DG9,A.DG8,A.DG7
  strand#3 DNA glyco-bond=s-s- nts=4 GGGG A.DG13,A.DG14,A.DG15,A.DG16
  strand#4 DNA glyco-bond=-s-s nts=4 GgGG A.DG22,A.BGM21,A.DG20,A.DG19

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3 stacking diagrams
 1  glyco-bond=s-s- groove=wnwn Major-->WC nts=4 GGGG A.DG1,A.DG10,A.DG13,A.DG22
2 glyco-bond=-s-s groove=wnwn WC-->Major nts=4 GGGg A.DG2,A.DG9,A.DG14,A.BGM21
step#1 mm(<>,outward) area=16.18 rise=3.43 twist=19.5

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 2  glyco-bond=-s-s groove=wnwn WC-->Major nts=4 GGGg A.DG2,A.DG9,A.DG14,A.BGM21
3 glyco-bond=s-s- groove=wnwn Major-->WC nts=4 GGGG A.DG3,A.DG8,A.DG15,A.DG20
step#2 pp(><,inward) area=15.26 rise=3.49 twist=35.9

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 3  glyco-bond=s-s- groove=wnwn Major-->WC nts=4 GGGG A.DG3,A.DG8,A.DG15,A.DG20
4 glyco-bond=-s-s groove=wnwn WC-->Major nts=4 GGGG A.DG4,A.DG7,A.DG16,A.DG19
step#3 mm(<>,outward) area=16.48 rise=3.39 twist=17.8

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List of 1 G4-stem [summary · schematics · tetrads · helices · costacks · homepage]

In DSSR, a G4-stem is defined as a G4-helix with backbone connectivity. Bulges are also allowed along each of the four strands.

Stem#1, 4 G-tetrad layers, 3 loops, INTRA-molecular, UDUD, anti-parallel, 4(-Lw-Ln-Lw), chair(2+2)

 1  glyco-bond=s-s- groove=wnwn Major-->WC nts=4 GGGG A.DG1,A.DG10,A.DG13,A.DG22
 2  glyco-bond=-s-s groove=wnwn WC-->Major nts=4 GGGg A.DG2,A.DG9,A.DG14,A.BGM21
 3  glyco-bond=s-s- groove=wnwn Major-->WC nts=4 GGGG A.DG3,A.DG8,A.DG15,A.DG20
 4  glyco-bond=-s-s groove=wnwn WC-->Major nts=4 GGGG A.DG4,A.DG7,A.DG16,A.DG19
  step#1  mm(<>,outward)  area=16.18 rise=3.43 twist=19.5
  step#2  pp(><,inward)   area=15.26 rise=3.49 twist=35.9
  step#3  mm(<>,outward)  area=16.48 rise=3.39 twist=17.8
  strand#1  U DNA glyco-bond=s-s- nts=4 GGGG A.DG1,A.DG2,A.DG3,A.DG4
  strand#2  D DNA glyco-bond=-s-s nts=4 GGGG A.DG10,A.DG9,A.DG8,A.DG7
  strand#3  U DNA glyco-bond=s-s- nts=4 GGGG A.DG13,A.DG14,A.DG15,A.DG16
  strand#4  D DNA glyco-bond=-s-s nts=4 GgGG A.DG22,A.BGM21,A.DG20,A.DG19
  loop#1 type=lateral   strands=[#1,#2] nts=2 CC A.DC5,A.DC6
  loop#2 type=lateral   strands=[#2,#3] nts=2 CC A.DC11,A.DC12
  loop#3 type=lateral   strands=[#3,#4] nts=2 CC A.DC17,A.DC18

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List of 0 G4 coaxial stacks [summary · schematics · tetrads · helices · stems · homepage]

List of 0 non-stem G4-loops (including the two closing Gs)