Summary information

PDB id
2km3
Class
DNA
Method
NMR
Summary
Structure of an intramolecular g-quadruplex containing a g.c.g.c tetrad formed by human telomeric variant ctaggg repeats
Reference
Lim KW, Alberti P, Guedin A, Lacroix L, Riou JF, Royle NJ, Mergny JL, Phan AT (2009): "Sequence variant (CTAGGG)n in the human telomere favors a G-quadruplex structure containing a G.C.G.C tetrad." Nucleic Acids Res., 37, 6239-6248. doi: 10.1093/nar/gkp630.
Abstract
Short contiguous arrays of variant CTAGGG repeats in the human telomere are unstable in the male germline and somatic cells, suggesting formation of unusual structures by this repeat type. Here, we report on the structure of an intramolecular G-quadruplex formed by DNA sequences containing four human telomeric variant CTAGGG repeats in potassium solution. Our results reveal a new robust antiparallel G-quadruplex fold involving two G-tetrads sandwiched between a G.C base pair and a G.C.G.C tetrad, which could represent a new platform for drug design targeted to human telomeric DNA.
G4 notes
2 G-tetrads, 1 G4 helix, 1 G4 stem, 2(+Ln+Lw+Ln), chair(2+2), UDUD

Base-block schematics in six views

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List of 2 G-tetrads

 1 glyco-bond=s-s- sugar=---- groove=wnwn planarity=0.294 type=other  nts=4 GGGG A.DG3,A.DG22,A.DG15,A.DG10
 2 glyco-bond=-s-s sugar=---- groove=wnwn planarity=0.167 type=other  nts=4 GGGG A.DG4,A.DG21,A.DG16,A.DG9

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=wnwn Major-->WC nts=4 GGGG A.DG3,A.DG22,A.DG15,A.DG10
 2  glyco-bond=-s-s sugar=---- groove=wnwn WC-->Major nts=4 GGGG A.DG4,A.DG21,A.DG16,A.DG9
  step#1  mm(<>,outward)  area=13.40 rise=3.55 twist=20.6
  strand#1 DNA glyco-bond=s- sugar=-- nts=2 GG A.DG3,A.DG4
  strand#2 DNA glyco-bond=-s sugar=-- nts=2 GG A.DG22,A.DG21
  strand#3 DNA glyco-bond=s- sugar=-- nts=2 GG A.DG15,A.DG16
  strand#4 DNA glyco-bond=-s sugar=-- nts=2 GG A.DG10,A.DG9

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1 stacking diagram 
 1  glyco-bond=s-s- sugar=---- groove=wnwn Major-->WC nts=4 GGGG A.DG3,A.DG22,A.DG15,A.DG10
 2  glyco-bond=-s-s sugar=---- groove=wnwn WC-->Major nts=4 GGGG A.DG4,A.DG21,A.DG16,A.DG9
  step#1  mm(<>,outward)  area=13.40 rise=3.55 twist=20.6

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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, UDUD, anti-parallel, 2(+Ln+Lw+Ln), chair(2+2)

 1  glyco-bond=s-s- sugar=---- groove=wnwn Major-->WC nts=4 GGGG A.DG3,A.DG22,A.DG15,A.DG10
 2  glyco-bond=-s-s sugar=---- groove=wnwn WC-->Major nts=4 GGGG A.DG4,A.DG21,A.DG16,A.DG9
  step#1  mm(<>,outward)  area=13.40 rise=3.55 twist=20.6
  strand#1  U DNA glyco-bond=s- sugar=-- nts=2 GG A.DG3,A.DG4
  strand#2  D DNA glyco-bond=-s sugar=-- nts=2 GG A.DG22,A.DG21
  strand#3  U DNA glyco-bond=s- sugar=-- nts=2 GG A.DG15,A.DG16
  strand#4  D DNA glyco-bond=-s sugar=-- nts=2 GG A.DG10,A.DG9
  loop#1 type=lateral   strands=[#1,#4] nts=4 CTAG A.DC5,A.DT6,A.DA7,A.DG8
  loop#2 type=lateral   strands=[#4,#3] nts=4 CTAG A.DC11,A.DT12,A.DA13,A.DG14
  loop#3 type=lateral   strands=[#3,#2] nts=4 CTAG A.DC17,A.DT18,A.DA19,A.DG20

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