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PDB-id
2mbj
Class
DNA
Method
NMR
Summary
Structure of an antiparallel (2+2) G-quadruplex formed by human telomeric repeats in na+ solution (with g22-to-brg substitution)
Reference
Lim, K.W., Ng, V.C., Martin-Pintado, N., Heddi, B., Phan, A.T.: (2013) "Structure of the human telomere in Na+ solution: an antiparallel (2+2) G-quadruplex scaffold reveals additional diversity." Nucleic Acids Res., 41, 10556-10562.
Abstract
Single-stranded DNA overhangs at the ends of human telomeric repeats are capable of adopting four-stranded G-quadruplex structures, which could serve as potential anticancer targets. Out of the five reported intramolecular human telomeric G-quadruplex structures, four were formed in the presence of K(+) ions and only one in the presence of Na(+) ions, leading often to a perception that this structural polymorphism occurs exclusively in the presence of K(+) but not Na(+). Here we present the structure of a new antiparallel (2+2) G-quadruplex formed by a derivative of a 27-nt human telomeric sequence in Na(+) solution, which comprises a novel core arrangement distinct from the known topologies. This structure complements the previously elucidated basket-type human telomeric G-quadruplex to serve as reference structures in Na(+)-containing environment. These structures, together with the coexistence of other conformations in Na(+) solution as observed by nuclear magnetic resonance spectroscopy, establish the polymorphic nature of human telomeric repeats beyond the influence of K(+) ions.
G4 notes
3 G-tetrads, 1 G4 helix, 1 G4 stem · 3(+Ln+P+Lw), (2+2), UUDD

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-- groove=-w-n planarity=0.121 type=planar nts=4 GgGG A.DG4,A.BGM22,A.DG18,A.DG12
 2 glyco-bond=ss-- groove=-w-n planarity=0.115 type=planar nts=4 GGGG A.DG5,A.DG23,A.DG17,A.DG11
 3 glyco-bond=--ss groove=-w-n planarity=0.103 type=planar nts=4 GGGG A.DG6,A.DG24,A.DG16,A.DG10

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-- groove=-w-n Major-->WC nts=4 GgGG A.DG4,A.BGM22,A.DG18,A.DG12
 2  glyco-bond=ss-- groove=-w-n Major-->WC nts=4 GGGG A.DG5,A.DG23,A.DG17,A.DG11
 3  glyco-bond=--ss groove=-w-n WC-->Major nts=4 GGGG A.DG6,A.DG24,A.DG16,A.DG10
  step#1  mp(<<,backward) area=13.76 rise=3.81 twist=29.6
  step#2  mm(<>,outward)  area=11.85 rise=3.83 twist=19.2
  strand#1 DNA glyco-bond=ss- nts=3 GGG A.DG4,A.DG5,A.DG6
  strand#2 DNA glyco-bond=ss- nts=3 gGG A.BGM22,A.DG23,A.DG24
  strand#3 DNA glyco-bond=--s nts=3 GGG A.DG18,A.DG17,A.DG16
  strand#4 DNA glyco-bond=--s nts=3 GGG A.DG12,A.DG11,A.DG10

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2 stacking diagrams
 1  glyco-bond=ss-- groove=-w-n Major-->WC nts=4 GgGG A.DG4,A.BGM22,A.DG18,A.DG12
2 glyco-bond=ss-- groove=-w-n Major-->WC nts=4 GGGG A.DG5,A.DG23,A.DG17,A.DG11
step#1 mp(<<,backward) area=13.76 rise=3.81 twist=29.6

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 2  glyco-bond=ss-- groove=-w-n Major-->WC nts=4 GGGG A.DG5,A.DG23,A.DG17,A.DG11
3 glyco-bond=--ss groove=-w-n WC-->Major nts=4 GGGG A.DG6,A.DG24,A.DG16,A.DG10
step#2 mm(<>,outward) area=11.85 rise=3.83 twist=19.2

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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, UUDD, anti-parallel, 3(+Ln+P+Lw), (2+2)

 1  glyco-bond=ss-- groove=-w-n Major-->WC nts=4 GgGG A.DG4,A.BGM22,A.DG18,A.DG12
 2  glyco-bond=ss-- groove=-w-n Major-->WC nts=4 GGGG A.DG5,A.DG23,A.DG17,A.DG11
 3  glyco-bond=--ss groove=-w-n WC-->Major nts=4 GGGG A.DG6,A.DG24,A.DG16,A.DG10
  step#1  mp(<<,backward) area=13.76 rise=3.81 twist=29.6
  step#2  mm(<>,outward)  area=11.85 rise=3.83 twist=19.2
  strand#1  U DNA glyco-bond=ss- nts=3 GGG A.DG4,A.DG5,A.DG6
  strand#2  U DNA glyco-bond=ss- nts=3 gGG A.BGM22,A.DG23,A.DG24
  strand#3  D DNA glyco-bond=--s nts=3 GGG A.DG18,A.DG17,A.DG16
  strand#4  D DNA glyco-bond=--s nts=3 GGG A.DG12,A.DG11,A.DG10
  loop#1 type=lateral   strands=[#1,#4] nts=3 TTA A.DT7,A.DT8,A.DA9
  loop#2 type=propeller strands=[#4,#3] nts=3 TTA A.DT13,A.DT14,A.DA15
  loop#3 type=lateral   strands=[#3,#2] nts=3 TTA A.DT19,A.DT20,A.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)