Summary information

PDB id
2kqg
Class
DNA
Method
NMR
Summary
A g-rich sequence within the c-kit oncogene promoter forms a parallel g-quadruplex having asymmetric g-tetrad dynamics
Reference
Hsu S-TD, Varnai P, Bugaut A, Reszka AP, Neidle S, Balasubramanian S (2009): "A G-rich sequence within the c-kit oncogene promoter forms a parallel G-quadruplex having asymmetric G-tetrad dynamics." J.Am.Chem.Soc., 131, 13399-13409. doi: 10.1021/ja904007p.
Abstract
Guanine-rich DNA sequences with the ability to form quadruplex structures are enriched in the promoter regions of protein-coding genes, particularly those of proto-oncogenes. G-quadruplexes are structurally polymorphic and their folding topologies can depend on the sample conditions. We report here on a structural study using solution state NMR spectroscopy of a second G-quadruplex-forming motif (c-kit2) that has been recently identified in the promoter region of the c-kit oncogene. In the presence of potassium ions, c-kit2 exists as an ensemble of structures that share the same parallel-stranded propeller-type conformations. Subtle differences in structural dynamics have been identified using hydrogen-deuterium exchange experiments by NMR spectroscopy, suggesting the coexistence of at least two structurally similar but dynamically distinct substates, which undergo slow interconversion on the NMR timescale.
G4 notes
3 G-tetrads, 1 G4 helix, 1 G4 stem, 3(-P-P-P), parallel(4+0), UUUU

Base-block schematics in six views

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List of 3 G-tetrads

 1 glyco-bond=---- sugar=.--- groove=---- planarity=0.276 type=other  nts=4 GGGG A.DG2,A.DG6,A.DG14,A.DG18
 2 glyco-bond=---- sugar=-.-- groove=---- planarity=0.173 type=other  nts=4 GGGG A.DG3,A.DG7,A.DG15,A.DG19
 3 glyco-bond=---- sugar=-3-- groove=---- planarity=0.255 type=other  nts=4 GGGG A.DG4,A.DG8,A.DG16,A.DG20

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

 1  glyco-bond=---- sugar=.--- groove=---- WC-->Major nts=4 GGGG A.DG2,A.DG6,A.DG14,A.DG18
 2  glyco-bond=---- sugar=-.-- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG7,A.DG15,A.DG19
 3  glyco-bond=---- sugar=-3-- groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG8,A.DG16,A.DG20
  step#1  pm(>>,forward)  area=19.15 rise=3.41 twist=21.0
  step#2  pm(>>,forward)  area=12.05 rise=3.47 twist=28.2
  strand#1 DNA glyco-bond=--- sugar=.-- nts=3 GGG A.DG2,A.DG3,A.DG4
  strand#2 DNA glyco-bond=--- sugar=-.3 nts=3 GGG A.DG6,A.DG7,A.DG8
  strand#3 DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG14,A.DG15,A.DG16
  strand#4 DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG18,A.DG19,A.DG20

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2 stacking diagrams
 1  glyco-bond=---- sugar=.--- groove=---- WC-->Major nts=4 GGGG A.DG2,A.DG6,A.DG14,A.DG18
2 glyco-bond=---- sugar=-.-- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG7,A.DG15,A.DG19
step#1 pm(>>,forward) area=19.15 rise=3.41 twist=21.0

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 2  glyco-bond=---- sugar=-.-- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG7,A.DG15,A.DG19
3 glyco-bond=---- sugar=-3-- groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG8,A.DG16,A.DG20
step#2 pm(>>,forward) area=12.05 rise=3.47 twist=28.2

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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, 3 G-tetrad layers, 3 loops, INTRA-molecular, UUUU, parallel, 3(-P-P-P), parallel(4+0)

 1  glyco-bond=---- sugar=.--- groove=---- WC-->Major nts=4 GGGG A.DG2,A.DG6,A.DG14,A.DG18
 2  glyco-bond=---- sugar=-.-- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG7,A.DG15,A.DG19
 3  glyco-bond=---- sugar=-3-- groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG8,A.DG16,A.DG20
  step#1  pm(>>,forward)  area=19.15 rise=3.41 twist=21.0
  step#2  pm(>>,forward)  area=12.05 rise=3.47 twist=28.2
  strand#1  U DNA glyco-bond=--- sugar=.-- nts=3 GGG A.DG2,A.DG3,A.DG4
  strand#2  U DNA glyco-bond=--- sugar=-.3 nts=3 GGG A.DG6,A.DG7,A.DG8
  strand#3  U DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG14,A.DG15,A.DG16
  strand#4  U DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG18,A.DG19,A.DG20
  loop#1 type=propeller strands=[#1,#2] nts=1 C A.DC5
  loop#2 type=propeller strands=[#2,#3] nts=5 CACGA A.DC9,A.DA10,A.DC11,A.DG12,A.DA13
  loop#3 type=propeller strands=[#3,#4] nts=1 A A.DA17

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