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

PDB-id
2kqh
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.-T.D., Varnai, P., Bugaut, A., Reszka, A.P., 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.
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 [summary · tetrads · helices · stems · costacks · homepage]

PyMOL session file PDB file View in 3Dmol.js

List of 3 G-tetrads [summary · schematics · helices · stems · costacks · homepage]

 1 glyco-bond=---- groove=---- planarity=0.219 type=other  nts=4 GGGG A.DG2,A.DG6,A.DG14,A.DG18
 2 glyco-bond=---- groove=---- planarity=0.335 type=other  nts=4 GGGG A.DG3,A.DG7,A.DG15,A.DG19
 3 glyco-bond=---- groove=---- planarity=0.522 type=bowl   nts=4 GGGG A.DG4,A.DG8,A.DG16,A.DG20

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

 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG2,A.DG6,A.DG14,A.DG18
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG7,A.DG15,A.DG19
 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG8,A.DG16,A.DG20
  step#1  pm(>>,forward)  area=13.62 rise=3.43 twist=26.6
  step#2  pm(>>,forward)  area=13.85 rise=3.59 twist=25.6
  strand#1 DNA glyco-bond=--- nts=3 GGG A.DG2,A.DG3,A.DG4
  strand#2 DNA glyco-bond=--- nts=3 GGG A.DG6,A.DG7,A.DG8
  strand#3 DNA glyco-bond=--- nts=3 GGG A.DG14,A.DG15,A.DG16
  strand#4 DNA glyco-bond=--- nts=3 GGG A.DG18,A.DG19,A.DG20

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2 stacking diagrams
 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG2,A.DG6,A.DG14,A.DG18
2 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG7,A.DG15,A.DG19
step#1 pm(>>,forward) area=13.62 rise=3.43 twist=26.6

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 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG7,A.DG15,A.DG19
3 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG8,A.DG16,A.DG20
step#2 pm(>>,forward) area=13.85 rise=3.59 twist=25.6

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

 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG2,A.DG6,A.DG14,A.DG18
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG7,A.DG15,A.DG19
 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG8,A.DG16,A.DG20
  step#1  pm(>>,forward)  area=13.62 rise=3.43 twist=26.6
  step#2  pm(>>,forward)  area=13.85 rise=3.59 twist=25.6
  strand#1  U DNA glyco-bond=--- nts=3 GGG A.DG2,A.DG3,A.DG4
  strand#2  U DNA glyco-bond=--- nts=3 GGG A.DG6,A.DG7,A.DG8
  strand#3  U DNA glyco-bond=--- nts=3 GGG A.DG14,A.DG15,A.DG16
  strand#4  U DNA glyco-bond=--- 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 CGCGA A.DC9,A.DG10,A.DC11,A.DG12,A.DA13
  loop#3 type=propeller strands=[#3,#4] nts=1 A A.DA17

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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)