Summary information

PDB id
7oqt
Class
DNA
Method
NMR
Summary
G-quadruplex structure of the c. elegans telomeric repeat: a two tetrads basket type conformation stabilised by a hoogsteen c-t base-pair
Reference
Marquevielle J, De Rache A, Vialet B, Morvan E, Mergny JL, Amrane S (2022): "G-quadruplex structure of the C. elegans telomeric repeat: a two tetrads basket type conformation stabilized by a non-canonical C-T base-pair." Nucleic Acids Res., 50, 7134-7146. doi: 10.1093/nar/gkac523.
Abstract
The Caenorhabditis elegans model has greatly contributed to the understanding of the role of G-quadruplexes in genomic instability. The GGCTTA repeats of the C. elegans telomeres resemble the GGGTTA repeats of the human telomeres. However, the comparison of telomeric sequences (Homo sapiens, Tetrahymena, Oxytricha, Bombyx mori and Giardia) revealed that small changes in these repeats can drastically change the topology of the folded G-quadruplex. In the present work we determined the structure adopted by the C. elegans telomeric sequence d[GG(CTTAGG)3]. The investigated C. elegans telomeric sequence is shown to fold into an intramolecular two G-tetrads basket type G-quadruplex structure that includes a C-T base pair in the diagonal loop. This work sheds light on the telomeric structure of the widely used C. elegans animal model.
G4 notes
2 G-tetrads, 1 G4 helix, 1 G4 stem, 2(-LwD+Ln), basket(2+2), UDDU

Base-block schematics in six views

PyMOL session file PDB file View in 3Dmol.js

List of 2 G-tetrads

 1 glyco-bond=s--s sugar=--.. groove=w-n- planarity=0.224 type=other  nts=4 GGGG A.DG1,A.DG8,A.DG20,A.DG13
 2 glyco-bond=-ss- sugar=---- groove=w-n- planarity=0.184 type=other  nts=4 GGGG A.DG2,A.DG7,A.DG19,A.DG14

List of 1 G4-helix

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, 2 G-tetrad layers, INTRA-molecular, with 1 stem

 1  glyco-bond=s--s sugar=--.. groove=w-n- Major-->WC nts=4 GGGG A.DG1,A.DG8,A.DG20,A.DG13
 2  glyco-bond=-ss- sugar=---- groove=w-n- WC-->Major nts=4 GGGG A.DG2,A.DG7,A.DG19,A.DG14
  step#1  mm(<>,outward)  area=10.14 rise=3.40 twist=21.2
  strand#1 DNA glyco-bond=s- sugar=-- nts=2 GG A.DG1,A.DG2
  strand#2 DNA glyco-bond=-s sugar=-- nts=2 GG A.DG8,A.DG7
  strand#3 DNA glyco-bond=-s sugar=.- nts=2 GG A.DG20,A.DG19
  strand#4 DNA glyco-bond=s- sugar=.- nts=2 GG A.DG13,A.DG14

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1 stacking diagram 
 1  glyco-bond=s--s sugar=--.. groove=w-n- Major-->WC nts=4 GGGG A.DG1,A.DG8,A.DG20,A.DG13
 2  glyco-bond=-ss- sugar=---- groove=w-n- WC-->Major nts=4 GGGG A.DG2,A.DG7,A.DG19,A.DG14
  step#1  mm(<>,outward)  area=10.14 rise=3.40 twist=21.2

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List of 1 G4-stem

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, 2 G-tetrad layers, 3 loops, INTRA-molecular, UDDU, anti-parallel, 2(-LwD+Ln), basket(2+2)

 1  glyco-bond=s--s sugar=--.. groove=w-n- Major-->WC nts=4 GGGG A.DG1,A.DG8,A.DG20,A.DG13
 2  glyco-bond=-ss- sugar=---- groove=w-n- WC-->Major nts=4 GGGG A.DG2,A.DG7,A.DG19,A.DG14
  step#1  mm(<>,outward)  area=10.14 rise=3.40 twist=21.2
  strand#1  U DNA glyco-bond=s- sugar=-- nts=2 GG A.DG1,A.DG2
  strand#2  D DNA glyco-bond=-s sugar=-- nts=2 GG A.DG8,A.DG7
  strand#3  D DNA glyco-bond=-s sugar=.- nts=2 GG A.DG20,A.DG19
  strand#4  U DNA glyco-bond=s- sugar=.- nts=2 GG A.DG13,A.DG14
  loop#1 type=lateral   strands=[#1,#2] nts=4 CTTA A.DC3,A.DT4,A.DT5,A.DA6
  loop#2 type=diagonal  strands=[#2,#4] nts=4 CTTA A.DC9,A.DT10,A.DT11,A.DA12
  loop#3 type=lateral   strands=[#4,#3] nts=4 CTTA A.DC15,A.DT16,A.DT17,A.DA18

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