Summary information

PDB id
1xce
Class
DNA
Method
NMR
Summary
Helica structure of DNA by design: the t(gggg)t hexad alignment
Reference
Webba da Silva M (2005): "Experimental Demonstration of T:(G:G:G):T Hexad and T:A:A:T Tetrad Alignments within a DNA Quadruplex Stem." Biochemistry, 44, 3754-3764. doi: 10.1021/bi0478190.
Abstract
A template-based approach was used to design unprecedented architectural motifs into a known DNA framework. The structure formed by the sequence d(GCGGTTGGAT) in 0.1 M Na(+) solution has been determined using molecular dynamics simulations constrained by distance and dihedral restraints derived from NMR experiments. The molecular topology has been previously observed for the sequence d(GCGGTGGAT) (Webba da Silva, M. (2003) Biochemistry 42, 14356-65). Insertion of a single thymine into the double chain reversal formed by the segment GGTGG results in the unprecedented experimental demonstration of a T:(G:G:G:G):T hexad. The bi-stranded hexad results from the pairing alignment of two G(T-G) triads. Each triad results from recognition of the sheared edge of a guanine by the Watson-Crick edge of a thymine of the segment GGTTGG. The alignment is stabilized by base-stacking of the thymine to the sugar pucker of the preceding thymine. The latter is involved in formation of the T:A:A:T tetrad alignment by forming a hydrogen bond with the free amino proton of a Watson-Crick aligned A:A mispair. We have thus established that residues in double chain reversal loops linking juxtaposed tetrads of a quadruplex stem may facilitate formation of yet unknown hydrogen bond alignments. By employing a systematic approach analysis of sequence motifs appearing in double chain reversals, bridging tetrad layers should allow for the prediction of topologies and architectural motifs appearing in biologically relevant genomic regions.
G4 notes
4 G-tetrads, 2 G4 helices, 2 G4 stems, parallel(4+0), UUUU

Base-block schematics in six views

PyMOL session file PDB file View in 3Dmol.js

List of 4 G-tetrads

 1 glyco-bond=---- sugar=.3-3 groove=---- planarity=0.280 type=other  nts=4 GGGG A.DG3,A.DG7,B.DG3,B.DG7
 2 glyco-bond=---- sugar=---- groove=---- planarity=0.040 type=planar nts=4 GGGG A.DG4,A.DG8,B.DG4,B.DG8
 3 glyco-bond=---- sugar=.3-3 groove=---- planarity=0.315 type=other  nts=4 GGGG C.DG3,C.DG7,D.DG3,D.DG7
 4 glyco-bond=---- sugar=---- groove=---- planarity=0.024 type=planar nts=4 GGGG C.DG4,C.DG8,D.DG4,D.DG8

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=.3-3 groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG7,B.DG3,B.DG7
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG8,B.DG4,B.DG8
  step#1  pm(>>,forward)  area=17.06 rise=3.10 twist=21.0
  strand#1 DNA glyco-bond=-- sugar=.- nts=2 GG A.DG3,A.DG4
  strand#2 DNA glyco-bond=-- sugar=3- nts=2 GG A.DG7,A.DG8
  strand#3 DNA glyco-bond=-- sugar=-- nts=2 GG B.DG3,B.DG4
  strand#4 DNA glyco-bond=-- sugar=3- nts=2 GG B.DG7,B.DG8

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1 stacking diagram 
 1  glyco-bond=---- sugar=.3-3 groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG7,B.DG3,B.DG7
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG8,B.DG4,B.DG8
  step#1  pm(>>,forward)  area=17.06 rise=3.10 twist=21.0

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

 1  glyco-bond=---- sugar=.3-3 groove=---- WC-->Major nts=4 GGGG C.DG3,C.DG7,D.DG3,D.DG7
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG C.DG4,C.DG8,D.DG4,D.DG8
  step#1  pm(>>,forward)  area=18.50 rise=3.20 twist=18.4
  strand#1 DNA glyco-bond=-- sugar=.- nts=2 GG C.DG3,C.DG4
  strand#2 DNA glyco-bond=-- sugar=3- nts=2 GG C.DG7,C.DG8
  strand#3 DNA glyco-bond=-- sugar=-- nts=2 GG D.DG3,D.DG4
  strand#4 DNA glyco-bond=-- sugar=3- nts=2 GG D.DG7,D.DG8

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1 stacking diagram 
 1  glyco-bond=---- sugar=.3-3 groove=---- WC-->Major nts=4 GGGG C.DG3,C.DG7,D.DG3,D.DG7
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG C.DG4,C.DG8,D.DG4,D.DG8
  step#1  pm(>>,forward)  area=18.50 rise=3.20 twist=18.4

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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=.3-3 groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG7,B.DG3,B.DG7
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG8,B.DG4,B.DG8
  step#1  pm(>>,forward)  area=17.06 rise=3.10 twist=21.0
  strand#1  U DNA glyco-bond=-- sugar=.- nts=2 GG A.DG3,A.DG4
  strand#2  U DNA glyco-bond=-- sugar=3- nts=2 GG A.DG7,A.DG8
  strand#3  U DNA glyco-bond=-- sugar=-- nts=2 GG B.DG3,B.DG4
  strand#4  U DNA glyco-bond=-- sugar=3- nts=2 GG B.DG7,B.DG8
  loop#1 type=propeller strands=[#1,#2] nts=2 TT A.DT5,A.DT6
  loop#2 type=propeller strands=[#3,#4] nts=2 TT B.DT5,B.DT6

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

 1  glyco-bond=---- sugar=.3-3 groove=---- WC-->Major nts=4 GGGG C.DG3,C.DG7,D.DG3,D.DG7
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG C.DG4,C.DG8,D.DG4,D.DG8
  step#1  pm(>>,forward)  area=18.50 rise=3.20 twist=18.4
  strand#1  U DNA glyco-bond=-- sugar=.- nts=2 GG C.DG3,C.DG4
  strand#2  U DNA glyco-bond=-- sugar=3- nts=2 GG C.DG7,C.DG8
  strand#3  U DNA glyco-bond=-- sugar=-- nts=2 GG D.DG3,D.DG4
  strand#4  U DNA glyco-bond=-- sugar=3- nts=2 GG D.DG7,D.DG8
  loop#1 type=propeller strands=[#1,#2] nts=2 TT C.DT5,C.DT6
  loop#2 type=propeller strands=[#3,#4] nts=2 TT D.DT5,D.DT6

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