Summary information [schematics · tetrads · helices · stems · costacks · homepage]

PDB-id
1oz8
Class
DNA
Method
NMR
Summary
Intramolecular higher-order packing of parallel quadruplexes comprising a g:g:g:g tetrad and a g(:a):g(:a):g(:a):g heptad of gga triplet repeat DNA
Reference
Matsugami, A., Okuizumi, T., Uesugi, S., Katahira, M.: (2003) "Intramolecular Higher Order Packing of Parallel Quadruplexes Comprising a G:G:G:G Tetrad and a G(:A):G(:A):G(:A):G Heptad of GGA Triplet Repeat DNA." J.BIOL.CHEM., 278, 28147-28153.
Abstract
GGA triplet repeats are widely dispersed throughout eukaryotic genomes and are frequently located within biologically important regions such as gene regulatory regions and recombination hot spot sites. We determined the structure of d(GGA)4 (12-mer) under physiological conditions and founded the formation of an intramolecular parallel quadruplex for the first time. Later, a similar architecture to that of the intramolecular parallel quadruplex was found for a telomere DNA in the crystalline state. Here, we have determined the structure of d(GGA)8 (24-mer) under physiological conditions. Two intramolecular parallel quadruplexes comprising a G:G:G:G tetrad and a G(:A):G(:A):G(:A):G heptad are formed in d(GGA)8. These quadruplexes are packed in a tail-to-tail manner. This is the first demonstration of the intramolecular higher order packing of quadruplexes at atomic resolution. K+ ions, but not Na+ ones, are critically required for the formation of this unique structure. The elucidated structure suggests the mechanisms underlying the biological events related to the GGA triplet repeat. Furthermore, in the light of the structure, the mode of the higher order packing of the telomere DNA is discussed.
G4 notes
3 G-tetrads, 1 G4 helix, 1 G4 stem · 2(-P-P-P), parallel(4+0), UUUU

Base-block schematics in six views [summary · tetrads · helices · stems · costacks · homepage]

PyMOL session file PDB file View in 3Dmol.js

List of 3 G-tetrads [summary · schematics · helices · stems · costacks · homepage]

 1 glyco-bond=---- groove=---- planarity=0.322 type=other  nts=4 GGGG A.DG1,A.DG4,A.DG7,A.DG10
 2 glyco-bond=---- groove=---- planarity=0.381 type=other  nts=4 GGGG A.DG13,A.DG16,A.DG19,A.DG22
 3 glyco-bond=---- groove=---- planarity=0.522 type=bowl   nts=4 GGGG A.DG14,A.DG17,A.DG20,A.DG23

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=---- groove=---- WC-->Major nts=4 GGGG A.DG1,A.DG4,A.DG7,A.DG10
 2  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG A.DG22,A.DG19,A.DG16,A.DG13
 3  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG A.DG23,A.DG20,A.DG17,A.DG14
  step#1  mm(<>,outward)  area=26.12 rise=3.52 twist=-1.3
  step#2  pm(>>,forward)  area=9.52  rise=3.27 twist=30.8
  strand#1 DNA glyco-bond=--- nts=3 GGG A.DG1,A.DG22,A.DG23
  strand#2 DNA glyco-bond=--- nts=3 GGG A.DG4,A.DG19,A.DG20
  strand#3 DNA glyco-bond=--- nts=3 GGG A.DG7,A.DG16,A.DG17
  strand#4 DNA glyco-bond=--- nts=3 GGG A.DG10,A.DG13,A.DG14

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2 stacking diagrams
 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG1,A.DG4,A.DG7,A.DG10
2 glyco-bond=---- groove=---- Major-->WC nts=4 GGGG A.DG22,A.DG19,A.DG16,A.DG13
step#1 mm(<>,outward) area=26.12 rise=3.52 twist=-1.3

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 2  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG A.DG22,A.DG19,A.DG16,A.DG13
3 glyco-bond=---- groove=---- Major-->WC nts=4 GGGG A.DG23,A.DG20,A.DG17,A.DG14
step#2 pm(>>,forward) area=9.52 rise=3.27 twist=30.8

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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, 2 G-tetrad layers, 3 loops, INTRA-molecular, UUUU, parallel, 2(-P-P-P), parallel(4+0)

 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG13,A.DG16,A.DG19,A.DG22
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG14,A.DG17,A.DG20,A.DG23
  step#1  pm(>>,forward)  area=9.52  rise=3.27 twist=30.8
  strand#1  U DNA glyco-bond=-- nts=2 GG A.DG13,A.DG14
  strand#2  U DNA glyco-bond=-- nts=2 GG A.DG16,A.DG17
  strand#3  U DNA glyco-bond=-- nts=2 GG A.DG19,A.DG20
  strand#4  U DNA glyco-bond=-- nts=2 GG A.DG22,A.DG23
  loop#1 type=propeller strands=[#1,#2] nts=1 A A.DA15
  loop#2 type=propeller strands=[#2,#3] nts=1 A A.DA18
  loop#3 type=propeller strands=[#3,#4] nts=1 A A.DA21

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List of 0 G4 coaxial stacks [summary · schematics · tetrads · helices · stems · homepage]

List of 3 non-stem G4-loops (including the two closing Gs)

 1 type=lateral   helix=#1 nts=4 GGAG A.DG1,A.DG2,A.DA3,A.DG4
 2 type=lateral   helix=#1 nts=4 GGAG A.DG4,A.DG5,A.DA6,A.DG7
 3 type=lateral   helix=#1 nts=4 GGAG A.DG7,A.DG8,A.DA9,A.DG10