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

PDB-id
2o3m
Class
DNA
Method
NMR
Summary
Monomeric g-DNA tetraplex from human c-kit promoter
Reference
Phan, A.T., Kuryavyi, V.V., Burge, S., Neidle, S., Patel, D.J.: (2007) "Structure of an unprecedented G-quadruplex scaffold in the human c-kit promoter." J.Am.Chem.Soc., 129, 4386-4392.
Abstract
The c-kit oncogene is an important target in the treatment of gastrointestinal tumors. A potential approach to inhibition of the expression of this gene involves selective stabilization of G-quadruplex structures that may be induced to form in the c-kit promoter region. Here we report on the structure of an unprecedented intramolecular G-quadruplex formed by a G-rich sequence in the c-kit promoter in K+ solution. The structure represents a new folding topology with several unique features. Most strikingly, an isolated guanine is involved in G-tetrad core formation, despite the presence of four three-guanine tracts. There are four loops: two single-residue double-chain-reversal loops, a two-residue loop, and a five-residue stem-loop, which contain base-pairing alignments. This unique structural scaffold provides a highly specific platform for the future design of ligands specifically targeted to the promoter DNA of c-kit.
G4 notes
3 G-tetrads, 1 G4 helix, 1 G4 stem · 2(-PX+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=0.084 type=planar nts=4 GGGG A.DG2,A.DG6,A.DG10,A.DG13
 2 glyco-bond=---- groove=---- planarity=0.112 type=planar nts=4 GGGG A.DG3,A.DG7,A.DG21,A.DG14
 3 glyco-bond=---- groove=---- planarity=0.084 type=planar nts=4 GGGG A.DG4,A.DG8,A.DG22,A.DG15

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.DG10,A.DG13
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG7,A.DG21,A.DG14
 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG8,A.DG22,A.DG15
  step#1  pm(>>,forward)  area=13.74 rise=3.14 twist=27.9
  step#2  pm(>>,forward)  area=10.77 rise=3.19 twist=32.0
  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.DG10,A.DG21,A.DG22
  strand#4 DNA glyco-bond=--- nts=3 GGG A.DG13,A.DG14,A.DG15

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2 stacking diagrams
 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG2,A.DG6,A.DG10,A.DG13
2 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG7,A.DG21,A.DG14
step#1 pm(>>,forward) area=13.74 rise=3.14 twist=27.9

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 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG7,A.DG21,A.DG14
3 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG8,A.DG22,A.DG15
step#2 pm(>>,forward) area=10.77 rise=3.19 twist=32.0

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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, 2 G-tetrad layers, 3 loops, INTRA-molecular, UUUU, parallel, 2(-PX+P), parallel(4+0)

 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG7,A.DG21,A.DG14
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG8,A.DG22,A.DG15
  step#1  pm(>>,forward)  area=10.77 rise=3.19 twist=32.0
  strand#1  U DNA glyco-bond=-- nts=2 GG A.DG3,A.DG4
  strand#2  U DNA glyco-bond=-- nts=2 GG A.DG7,A.DG8
  strand#3  U DNA glyco-bond=-- nts=2 GG A.DG21,A.DG22
  strand#4  U DNA glyco-bond=-- nts=2 GG A.DG14,A.DG15
  loop#1 type=propeller strands=[#1,#2] nts=2 AG A.DA5,A.DG6
  loop#2 type=diag-prop strands=[#2,#4] nts=5 CGCTG A.DC9,A.DG10,A.DC11,A.DT12,A.DG13
  loop#3 type=propeller strands=[#4,#3] nts=5 AGGAG A.DA16,A.DG17,A.DG18,A.DA19,A.DG20

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List of 0 G4 coaxial stacks [summary · schematics · tetrads · helices · stems · homepage]

List of 2 non-stem G4-loops (including the two closing Gs)

 1* type=V-shaped  helix=#1 nts=5 GGGCG A.DG6,A.DG7,A.DG8,A.DC9,A.DG10
 2 type=lateral   helix=#1 nts=4 GCTG A.DG10,A.DC11,A.DT12,A.DG13