Summary information and primary citation

PDB-id
2kka
Class
DNA
Method
NMR
Summary
Human telomere DNA two-tetrad quadruplex structure in k+ solution
Reference
Zhang Z, Dai J, Veliath E, Jones RA, Yang D (2010): "Structure of a two-G-tetrad intramolecular G-quadruplex formed by a variant human telomeric sequence in K+ solution: insights into the interconversion of human telomeric G-quadruplex structures." Nucleic Acids Res., 38, 1009-1021. doi: 10.1093/nar/gkp1029.
Abstract
Human telomeric DNA G-quadruplex has been considered as an attractive target for cancer therapeutic intervention. The telomeric sequence shows intrinsic structure polymorphism. Here we report a novel intramolecular G-quadruplex structure formed by a variant human telomeric sequence in K(+) solution. This sequence forms a basket-type intramolecular G-quadruplex with only two G-tetrads but multiple-layer capping structures formed by loop residues. While it is shown that this structure can only be detected in the specifically truncated telomeric sequences without any 5'-flanking residues, our results suggest that this two-G-tetrad conformation is likely to be an intermediate form of the interconversion of different telomeric G-quadruplex conformations.
G4 notes
2 G-tetrads, 1 G4 helix, 1 G4 stem, UDDU, anti-parallel:basket, 2+2, 2(-LwD+Ln)

Cartoon-block schematics in six views (download the tarball)

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List of 2 G-tetrads

 1 glyco-bond=s--s sugar=3..- groove=w-n- planarity=0.061 type=planar N- nts=4 GGGG A.DG2,A.DG9,A.DG21,A.DG15
 2 glyco-bond=-ss- sugar=.3.. groove=w-n- planarity=0.084 type=planar N+ nts=4 GGGG A.DG3,A.DG8,A.DG20,A.DG16

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-tetrads, INTRA-molecular, with 1 stem
 1  glyco-bond=s--s sugar=3..- groove=w-n- Major-->WC N- nts=4 GGGG A.DG2,A.DG9,A.DG21,A.DG15
 2  glyco-bond=-ss- sugar=.3.. groove=w-n- WC-->Major N+ nts=4 GGGG A.DG3,A.DG8,A.DG20,A.DG16
  step#1  mm(<>,outward)  area=16.71 rise=4.21 twist=14.5
  strand#1 DNA glyco-bond=s- sugar=3. nts=2 GG A.DG2,A.DG3
  strand#2 DNA glyco-bond=-s sugar=.3 nts=2 GG A.DG9,A.DG8
  strand#3 DNA glyco-bond=-s sugar=.. nts=2 GG A.DG21,A.DG20
  strand#4 DNA glyco-bond=s- sugar=-. nts=2 GG A.DG15,A.DG16

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1 stacking diagram 
 1  glyco-bond=s--s sugar=3..- groove=w-n- Major-->WC N- nts=4 GGGG A.DG2,A.DG9,A.DG21,A.DG15
 2  glyco-bond=-ss- sugar=.3.. groove=w-n- WC-->Major N+ nts=4 GGGG A.DG3,A.DG8,A.DG20,A.DG16
  step#1  mm(<>,outward)  area=16.71 rise=4.21 twist=14.5

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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-tetrads, 3 loops, INTRA-molecular, UDDU, anti-parallel:basket, 2+2, 2(-LwD+Ln)
 1  glyco-bond=s--s sugar=3..- groove=w-n- Major-->WC N- nts=4 GGGG A.DG2,A.DG9,A.DG21,A.DG15
 2  glyco-bond=-ss- sugar=.3.. groove=w-n- WC-->Major N+ nts=4 GGGG A.DG3,A.DG8,A.DG20,A.DG16
  step#1  mm(<>,outward)  area=16.71 rise=4.21 twist=14.5
  strand#1  U DNA glyco-bond=s- sugar=3. nts=2 GG A.DG2,A.DG3
  strand#2  D DNA glyco-bond=-s sugar=.3 nts=2 GG A.DG9,A.DG8
  strand#3  D DNA glyco-bond=-s sugar=.. nts=2 GG A.DG21,A.DG20
  strand#4  U DNA glyco-bond=s- sugar=-. nts=2 GG A.DG15,A.DG16
  loop#1 type=lateral   strands=[#1,#2] nts=4 GTTA A.DG4,A.DT5,A.DT6,A.DA7
  loop#2 type=diagonal  strands=[#2,#4] nts=5 GTTAg A.DG10,A.DT11,A.DT12,A.DA13,A.DI14
  loop#3 type=lateral   strands=[#4,#3] nts=3 TTA A.DT17,A.DT18,A.DA19

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