Summary information

PDB id
1nyd
Class
DNA
Method
NMR
Summary
Solution structure of DNA quadruplex gcggtggat
Reference
Webba da Silva M (2003): "Association of DNA quadruplexes through G:C:G:C tetrads. Solution structure of d(GCGGTGGAT)." Biochemistry, 42, 14356-14365. doi: 10.1021/bi0355185.
Abstract
The structure formed by the DNA sequence d(GCGGTGGAT) in a 100 mM Na(+) solution has been determined using molecular dynamics calculations constrained by distance and dihedral restraints derived from NMR experiments performed at isotopic natural abundance. The sequence folds into a dimer of dimers. Each symmetry-related half contains two parallel stranded G:G:G:G tetrads flanked by an A:A mismatch and by four-stranded G:C:G:C tetrads. Each of the two juxtaposed G:C:G:C tetrads is composed of alternating antiparallel strands from the two halves of the dimer. For each single strand, a thymine intersperses a double chain reversal connecting the juxtaposed G:G:G:G tetrads. This architecture has potential implications in genetic recombination. It suggests a pathway for oligomerization involving association of quadruplex entities through GpC steps.
G4 notes
4 G-tetrads, 2 G4 helices, 2 G4 stems, parallel(4+0), UUUU

Base-block schematics in six views

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List of 4 G-tetrads

 1 glyco-bond=---- sugar=---- groove=---- planarity=0.139 type=planar nts=4 GGGG A.DG3,A.DG6,B.DG3,B.DG6
 2 glyco-bond=---- sugar=---- groove=---- planarity=0.053 type=planar nts=4 GGGG A.DG4,A.DG7,B.DG4,B.DG7
 3 glyco-bond=---- sugar=---- groove=---- planarity=0.139 type=planar nts=4 GGGG C.DG3,C.DG6,D.DG3,D.DG6
 4 glyco-bond=---- sugar=---- groove=---- planarity=0.053 type=planar nts=4 GGGG C.DG4,C.DG7,D.DG4,D.DG7

List of 2 G4-helices

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, 2 G-tetrad layers, inter-molecular, with 1 stem

 1  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG6,B.DG3,B.DG6
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG7,B.DG4,B.DG7
  step#1  pm(>>,forward)  area=13.01 rise=3.12 twist=30.8
  strand#1 DNA glyco-bond=-- sugar=-- nts=2 GG A.DG3,A.DG4
  strand#2 DNA glyco-bond=-- sugar=-- nts=2 GG A.DG6,A.DG7
  strand#3 DNA glyco-bond=-- sugar=-- nts=2 GG B.DG3,B.DG4
  strand#4 DNA glyco-bond=-- sugar=-- nts=2 GG B.DG6,B.DG7

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1 stacking diagram 
 1  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG6,B.DG3,B.DG6
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG7,B.DG4,B.DG7
  step#1  pm(>>,forward)  area=13.01 rise=3.12 twist=30.8

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Helix#2, 2 G-tetrad layers, inter-molecular, with 1 stem

 1  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG C.DG3,C.DG6,D.DG3,D.DG6
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG C.DG4,C.DG7,D.DG4,D.DG7
  step#1  pm(>>,forward)  area=13.01 rise=3.12 twist=30.9
  strand#1 DNA glyco-bond=-- sugar=-- nts=2 GG C.DG3,C.DG4
  strand#2 DNA glyco-bond=-- sugar=-- nts=2 GG C.DG6,C.DG7
  strand#3 DNA glyco-bond=-- sugar=-- nts=2 GG D.DG3,D.DG4
  strand#4 DNA glyco-bond=-- sugar=-- nts=2 GG D.DG6,D.DG7

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1 stacking diagram 
 1  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG C.DG3,C.DG6,D.DG3,D.DG6
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG C.DG4,C.DG7,D.DG4,D.DG7
  step#1  pm(>>,forward)  area=13.01 rise=3.12 twist=30.9

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List of 2 G4-stems

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, 2 loops, inter-molecular, UUUU, parallel, parallel(4+0)

 1  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG6,B.DG3,B.DG6
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG7,B.DG4,B.DG7
  step#1  pm(>>,forward)  area=13.01 rise=3.12 twist=30.8
  strand#1  U DNA glyco-bond=-- sugar=-- nts=2 GG A.DG3,A.DG4
  strand#2  U DNA glyco-bond=-- sugar=-- nts=2 GG A.DG6,A.DG7
  strand#3  U DNA glyco-bond=-- sugar=-- nts=2 GG B.DG3,B.DG4
  strand#4  U DNA glyco-bond=-- sugar=-- nts=2 GG B.DG6,B.DG7
  loop#1 type=propeller strands=[#1,#2] nts=1 T A.DT5
  loop#2 type=propeller strands=[#3,#4] nts=1 T B.DT5

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Stem#2, 2 G-tetrad layers, 2 loops, inter-molecular, UUUU, parallel, parallel(4+0)

 1  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG C.DG3,C.DG6,D.DG3,D.DG6
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG C.DG4,C.DG7,D.DG4,D.DG7
  step#1  pm(>>,forward)  area=13.01 rise=3.12 twist=30.9
  strand#1  U DNA glyco-bond=-- sugar=-- nts=2 GG C.DG3,C.DG4
  strand#2  U DNA glyco-bond=-- sugar=-- nts=2 GG C.DG6,C.DG7
  strand#3  U DNA glyco-bond=-- sugar=-- nts=2 GG D.DG3,D.DG4
  strand#4  U DNA glyco-bond=-- sugar=-- nts=2 GG D.DG6,D.DG7
  loop#1 type=propeller strands=[#1,#2] nts=1 T C.DT5
  loop#2 type=propeller strands=[#3,#4] nts=1 T D.DT5

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