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PDB-id
2hy9
Class
DNA
Method
NMR
Summary
Human telomere DNA quadruplex structure in k+ solution hybrid-1 form
Reference
Dai, J., Punchihewa, C., Ambrus, A., Chen, D., Jones, R.A., Yang, D.: (2007) "Structure of the intramolecular human telomeric G-quadruplex in potassium solution: a novel adenine triple formation." Nucleic Acids Res., 35, 2440-2450.
Abstract
We report the NMR solution structure of the intramolecular G-quadruplex formed in human telomeric DNA in K(+). The hybrid-type telomeric G-quadruplex consists of three G-tetrads linked with mixed parallel-antiparallel G-strands, with the bottom two G-tetrads having the same G-arrangement (anti:anti:syn:anti) and the top G-tetrad having the reversed G-arrangement (syn:syn:anti:syn). The three TTA loop segments adopt different conformations, with the first TTA assuming a double-chain-reversal loop conformation, and the second and third TTA assuming lateral loop conformations. The NMR structure is very well defined, including the three TTA loops and the two flanking sequences at 5'- and 3'-ends. Our study indicates that the three loop regions interact with the core G-tetrads in a specific way that defines and stabilizes the unique human telomeric G-quadruplex structure in K(+). Significantly, a novel adenine triple platform is formed with three naturally occurring adenine residues, A21, A3 and A9, capping the top tetrad of the hybrid-type telomeric G-quadruplex. This adenine triple is likely to play an important role in the formation of a stable human telomeric G-quadruplex structure in K(+). The unique human telomeric G-quadruplex structure formed in K(+) suggests that it can be specifically targeted for anticancer drug design.
G4 notes
3 G-tetrads, 1 G4 helix, 1 G4 stem · 3(-P-Lw-Ln), hybrid-1(3+1), UUDU

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=ss-s groove=-wn- planarity=0.077 type=planar nts=4 GGGG 1.DG4,1.DG10,1.DG18,1.DG22
 2 glyco-bond=--s- groove=-wn- planarity=0.066 type=planar nts=4 GGGG 1.DG5,1.DG11,1.DG17,1.DG23
 3 glyco-bond=--s- groove=-wn- planarity=0.076 type=planar nts=4 GGGG 1.DG6,1.DG12,1.DG16,1.DG24

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=ss-s groove=-wn- Major-->WC nts=4 GGGG 1.DG4,1.DG10,1.DG18,1.DG22
 2  glyco-bond=--s- groove=-wn- WC-->Major nts=4 GGGG 1.DG5,1.DG11,1.DG17,1.DG23
 3  glyco-bond=--s- groove=-wn- WC-->Major nts=4 GGGG 1.DG6,1.DG12,1.DG16,1.DG24
  step#1  mm(<>,outward)  area=13.69 rise=3.15 twist=18.9
  step#2  pm(>>,forward)  area=13.40 rise=3.07 twist=27.8
  strand#1 DNA glyco-bond=s-- nts=3 GGG 1.DG4,1.DG5,1.DG6
  strand#2 DNA glyco-bond=s-- nts=3 GGG 1.DG10,1.DG11,1.DG12
  strand#3 DNA glyco-bond=-ss nts=3 GGG 1.DG18,1.DG17,1.DG16
  strand#4 DNA glyco-bond=s-- nts=3 GGG 1.DG22,1.DG23,1.DG24

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2 stacking diagrams
 1  glyco-bond=ss-s groove=-wn- Major-->WC nts=4 GGGG 1.DG4,1.DG10,1.DG18,1.DG22
2 glyco-bond=--s- groove=-wn- WC-->Major nts=4 GGGG 1.DG5,1.DG11,1.DG17,1.DG23
step#1 mm(<>,outward) area=13.69 rise=3.15 twist=18.9

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 2  glyco-bond=--s- groove=-wn- WC-->Major nts=4 GGGG 1.DG5,1.DG11,1.DG17,1.DG23
3 glyco-bond=--s- groove=-wn- WC-->Major nts=4 GGGG 1.DG6,1.DG12,1.DG16,1.DG24
step#2 pm(>>,forward) area=13.40 rise=3.07 twist=27.8

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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, UUDU, anti-parallel, 3(-P-Lw-Ln), hybrid-1(3+1)

 1  glyco-bond=ss-s groove=-wn- Major-->WC nts=4 GGGG 1.DG4,1.DG10,1.DG18,1.DG22
 2  glyco-bond=--s- groove=-wn- WC-->Major nts=4 GGGG 1.DG5,1.DG11,1.DG17,1.DG23
 3  glyco-bond=--s- groove=-wn- WC-->Major nts=4 GGGG 1.DG6,1.DG12,1.DG16,1.DG24
  step#1  mm(<>,outward)  area=13.69 rise=3.15 twist=18.9
  step#2  pm(>>,forward)  area=13.40 rise=3.07 twist=27.8
  strand#1  U DNA glyco-bond=s-- nts=3 GGG 1.DG4,1.DG5,1.DG6
  strand#2  U DNA glyco-bond=s-- nts=3 GGG 1.DG10,1.DG11,1.DG12
  strand#3  D DNA glyco-bond=-ss nts=3 GGG 1.DG18,1.DG17,1.DG16
  strand#4  U DNA glyco-bond=s-- nts=3 GGG 1.DG22,1.DG23,1.DG24
  loop#1 type=propeller strands=[#1,#2] nts=3 TTA 1.DT7,1.DT8,1.DA9
  loop#2 type=lateral   strands=[#2,#3] nts=3 TTA 1.DT13,1.DT14,1.DA15
  loop#3 type=lateral   strands=[#3,#4] nts=3 TTA 1.DT19,1.DT20,1.DA21

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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)