Summary information and primary citation

PDB-id
1s45
Class
DNA
Method
X-ray (2.2 Å)
Summary
Crystal structure analysis of the DNA quadruplex d(tggggt) s1
Reference
Caceres C, Wright G, Gouyette C, Parkinson G, Subirana JA (2004): "A Thymine tetrad in d(TGGGGT) quadruplexes stabilized with Tl+1/Na+1 ions." Nucleic Acids Res., 32, 1097-1102. doi: 10.1093/nar/gkh269.
Abstract
We report two new structures of the quadruplex d(TGGGGT)4 obtained by single crystal X-ray diffraction. In one of them a thymine tetrad is found. Thus the yeast telomere sequences d(TG1-3) might be able to form continuous quadruplex structures, involving both guanine and thymine tetrads. Our study also shows substantial differences in the arrangement of thymines when compared with previous studies. We find five different types of organization: (i) groove binding with hydrogen bonds to guanines from a neighbour quadruplex; (ii) partially ordered groove binding, without any hydrogen bond; (iii) stacked thymine triads, formed at the 3'ends of the quadruplexes; (iv) a thymine tetrad between two guanine tetrads. Thymines are stabilized in pairs by single hydrogen bonds. A central sodium ion interacts with two thymines and contributes to the tetrad structure. (v) Completely disordered thymines which do not show any clear location in the crystal. The tetrads are stabilized by either Na+ or Tl+ ions. We show that by using MAD methods, Tl+ can be unambiguously located and distinguished from Na+. We can thus determine the preference for either ion in each ionic site of the structure under the conditions used by us.
G4 notes
4 G-tetrads, 1 G4 helix, 1 G4 stem, UUUU, parallel, 4+0

Cartoon-block schematics in six views (download the tarball)

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List of 4 G-tetrads

 1 glyco-bond=---- sugar=3333 groove=---- planarity=0.098 type=planar -- nts=4 GGGG 1:A.DG182,1:D.DG512,1:C.DG402,1:B.DG292
 2 glyco-bond=---- sugar=---- groove=---- planarity=0.218 type=bowl   -- nts=4 GGGG 1:A.DG183,1:D.DG513,1:C.DG403,1:B.DG293
 3 glyco-bond=---- sugar=---- groove=---- planarity=0.191 type=other  -- nts=4 GGGG 1:A.DG184,1:D.DG514,1:C.DG404,1:B.DG294
 4 glyco-bond=---- sugar=---- groove=---- planarity=0.247 type=bowl   -- nts=4 GGGG 1:A.DG185,1:D.DG515,1:C.DG405,1:B.DG295

List of 1 G4-helix

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, 4 G-tetrads, inter-molecular, with 1 stem
 1  glyco-bond=---- sugar=3333 groove=---- WC-->Major -- nts=4 GGGG 1:A.DG182,1:D.DG512,1:C.DG402,1:B.DG292
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:A.DG183,1:D.DG513,1:C.DG403,1:B.DG293
 3  glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:A.DG184,1:D.DG514,1:C.DG404,1:B.DG294
 4  glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:A.DG185,1:D.DG515,1:C.DG405,1:B.DG295
  step#1  pm(>>,forward)  area=9.60  rise=3.57 twist=28.9
  step#2  pm(>>,forward)  area=9.27  rise=3.40 twist=31.8
  step#3  pm(>>,forward)  area=13.37 rise=3.37 twist=25.8
  strand#1 DNA glyco-bond=---- sugar=3--- nts=4 GGGG 1:A.DG182,1:A.DG183,1:A.DG184,1:A.DG185
  strand#2 DNA glyco-bond=---- sugar=3--- nts=4 GGGG 1:D.DG512,1:D.DG513,1:D.DG514,1:D.DG515
  strand#3 DNA glyco-bond=---- sugar=3--- nts=4 GGGG 1:C.DG402,1:C.DG403,1:C.DG404,1:C.DG405
  strand#4 DNA glyco-bond=---- sugar=3--- nts=4 GGGG 1:B.DG292,1:B.DG293,1:B.DG294,1:B.DG295

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3 stacking diagrams 
 1  glyco-bond=---- sugar=3333 groove=---- WC-->Major -- nts=4 GGGG 1:A.DG182,1:D.DG512,1:C.DG402,1:B.DG292
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:A.DG183,1:D.DG513,1:C.DG403,1:B.DG293
  step#1  pm(>>,forward)  area=9.60  rise=3.57 twist=28.9

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 2  glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:A.DG183,1:D.DG513,1:C.DG403,1:B.DG293
 3  glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:A.DG184,1:D.DG514,1:C.DG404,1:B.DG294
  step#2  pm(>>,forward)  area=9.27  rise=3.40 twist=31.8

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 3  glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:A.DG184,1:D.DG514,1:C.DG404,1:B.DG294
 4  glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:A.DG185,1:D.DG515,1:C.DG405,1:B.DG295
  step#3  pm(>>,forward)  area=13.37 rise=3.37 twist=25.8

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List of 1 G4-stem

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, 4 G-tetrads, 0 loops, inter-molecular, UUUU, parallel, 4+0
 1  glyco-bond=---- sugar=3333 groove=---- WC-->Major -- nts=4 GGGG 1:A.DG182,1:D.DG512,1:C.DG402,1:B.DG292
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:A.DG183,1:D.DG513,1:C.DG403,1:B.DG293
 3  glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:A.DG184,1:D.DG514,1:C.DG404,1:B.DG294
 4  glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:A.DG185,1:D.DG515,1:C.DG405,1:B.DG295
  step#1  pm(>>,forward)  area=9.60  rise=3.57 twist=28.9
  step#2  pm(>>,forward)  area=9.27  rise=3.40 twist=31.8
  step#3  pm(>>,forward)  area=13.37 rise=3.37 twist=25.8
  strand#1  U DNA glyco-bond=---- sugar=3--- nts=4 GGGG 1:A.DG182,1:A.DG183,1:A.DG184,1:A.DG185
  strand#2  U DNA glyco-bond=---- sugar=3--- nts=4 GGGG 1:D.DG512,1:D.DG513,1:D.DG514,1:D.DG515
  strand#3  U DNA glyco-bond=---- sugar=3--- nts=4 GGGG 1:C.DG402,1:C.DG403,1:C.DG404,1:C.DG405
  strand#4  U DNA glyco-bond=---- sugar=3--- nts=4 GGGG 1:B.DG292,1:B.DG293,1:B.DG294,1:B.DG295

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