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PDB-id
2l88
Class
DNA
Method
NMR
Summary
Solution structure of all parallel G-quadruplex formed by the oncogene ret promoter sequence
Reference
Tong, X., Lan, W., Zhang, X., Wu, H., Liu, M., Cao, C.: (2011) "Solution structure of all parallel G-quadruplex formed by the oncogene RET promoter sequence." Nucleic Acids Res., 39, 6753-6763.
Abstract
RET protein functions as a receptor-type tyrosine kinase and has been found to be aberrantly expressed in a wide range of human diseases. A highly GC-rich region upstream of the promoter plays an important role in the transcriptional regulation of RET. Here, we report the NMR solution structure of the major intramolecular G-quadruplex formed on the G-rich strand of this region in K(+) solution. The overall G-quadruplex is composed of three stacked G-tetrad and four syn guanines, which shows distinct features for all parallel-stranded folding topology. The core structure contains one G-tetrad with all syn guanines and two other with all anti-guanines. There are three double-chain reversal loops: the first and the third loops are made of 3 nt G-C-G segments, while the second one contains only 1 nt C10. These loops interact with the core G-tetrads in a specific way that defines and stabilizes the overall G-quadruplex structure and their conformations are in accord with the experimental mutations. The distinct RET promoter G-quadruplex structure suggests that it can be specifically involved in gene regulation and can be an attractive target for pathway-specific drug design.
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]

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

 1 glyco-bond=ssss groove=---- planarity=0.121 type=planar nts=4 GGGG A.DG1,A.DG7,A.DG11,A.DG17
 2 glyco-bond=---- groove=---- planarity=0.136 type=planar nts=4 GGGG A.DG2,A.DG8,A.DG12,A.DG18
 3 glyco-bond=---- groove=---- planarity=0.256 type=other  nts=4 GGGG A.DG3,A.DG9,A.DG13,A.DG19

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=ssss groove=---- Major-->WC nts=4 GGGG A.DG1,A.DG7,A.DG11,A.DG17
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG2,A.DG8,A.DG12,A.DG18
 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG9,A.DG13,A.DG19
  step#1  mm(<>,outward)  area=9.87  rise=3.95 twist=20.0
  step#2  pm(>>,forward)  area=17.79 rise=3.89 twist=20.7
  strand#1 DNA glyco-bond=s-- nts=3 GGG A.DG1,A.DG2,A.DG3
  strand#2 DNA glyco-bond=s-- nts=3 GGG A.DG7,A.DG8,A.DG9
  strand#3 DNA glyco-bond=s-- nts=3 GGG A.DG11,A.DG12,A.DG13
  strand#4 DNA glyco-bond=s-- nts=3 GGG A.DG17,A.DG18,A.DG19

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2 stacking diagrams
 1  glyco-bond=ssss groove=---- Major-->WC nts=4 GGGG A.DG1,A.DG7,A.DG11,A.DG17
2 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG2,A.DG8,A.DG12,A.DG18
step#1 mm(<>,outward) area=9.87 rise=3.95 twist=20.0

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 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG2,A.DG8,A.DG12,A.DG18
3 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG9,A.DG13,A.DG19
step#2 pm(>>,forward) area=17.79 rise=3.89 twist=20.7

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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=ssss groove=---- Major-->WC nts=4 GGGG A.DG1,A.DG7,A.DG11,A.DG17
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG2,A.DG8,A.DG12,A.DG18
 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG9,A.DG13,A.DG19
  step#1  mm(<>,outward)  area=9.87  rise=3.95 twist=20.0
  step#2  pm(>>,forward)  area=17.79 rise=3.89 twist=20.7
  strand#1  U DNA glyco-bond=s-- nts=3 GGG A.DG1,A.DG2,A.DG3
  strand#2  U DNA glyco-bond=s-- nts=3 GGG A.DG7,A.DG8,A.DG9
  strand#3  U DNA glyco-bond=s-- nts=3 GGG A.DG11,A.DG12,A.DG13
  strand#4  U DNA glyco-bond=s-- nts=3 GGG A.DG17,A.DG18,A.DG19
  loop#1 type=propeller strands=[#1,#2] nts=3 GCG A.DG4,A.DC5,A.DG6
  loop#2 type=propeller strands=[#2,#3] nts=1 C A.DC10
  loop#3 type=propeller strands=[#3,#4] nts=3 GCG A.DG14,A.DC15,A.DG16

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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)