Summary information

PDB id
6syk
Class
DNA
Method
NMR
Summary
Guanine-rich oligonucleotide with 5'- and 3'-gc ends form g-quadruplex with a(gggg)a hexad, gcgc- and g-quartets and two symmetric gg and aa base pair
Reference
Pavc D, Wang B, Spindler L, Drevensek-Olenik I, Plavec J, Sket P (2020): "GC ends control topology of DNA G-quadruplexes and their cation-dependent assembly." Nucleic Acids Res., 48, 2749-2761. doi: 10.1093/nar/gkaa058.
Abstract
GCn and GCnCG, where n = (G2AG4AG2), fold into well-defined, dimeric G-quadruplexes with unprecedented folding topologies in the presence of Na+ ions as revealed by nuclear magnetic resonance spectroscopy. Both G-quadruplexes exhibit unique combination of structural elements among which are two G-quartets, A(GGGG)A hexad and GCGC-quartet. Detailed structural characterization uncovered the crucial role of 5'-GC ends in formation of GCn and GCnCG G-quadruplexes. Folding in the presence of 15NH4+ and K+ ions leads to 3'-3' stacking of terminal G-quartets of GCn G-quadruplexes, while 3'-GC overhangs in GCnCG prevent dimerization. Results of the present study expand repertoire of possible G-quadruplex structures. This knowledge will be useful in DNA sequence design for nanotechnological applications that may require specific folding topology and multimerization properties.
G4 notes
3 G-tetrads, 1 G4 helix, 1 G4 stem, parallel(4+0), UUUU

Base-block schematics in six views

PyMOL session file PDB file View in 3Dmol.js

List of 3 G-tetrads

 1 glyco-bond=s-s- sugar=---- groove=wnwn planarity=0.291 type=other  nts=4 GGGG A.DG1,B.DG7,B.DG1,A.DG7
 2 glyco-bond=---- sugar=---- groove=---- planarity=0.509 type=bowl-2 nts=4 GGGG A.DG8,A.DG11,B.DG8,B.DG11
 3 glyco-bond=---- sugar=---- groove=---- planarity=0.625 type=bowl   nts=4 GGGG A.DG9,A.DG12,B.DG9,B.DG12

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

 1  glyco-bond=s-s- sugar=---- groove=wnwn Major-->WC nts=4 GGGG A.DG1,B.DG7,B.DG1,A.DG7
 2  glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG B.DG11,B.DG8,A.DG11,A.DG8
 3  glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG B.DG12,B.DG9,A.DG12,A.DG9
  step#1  pm(>>,forward)  area=8.84  rise=3.42 twist=32.4
  step#2  pm(>>,forward)  area=14.11 rise=3.40 twist=24.8
  strand#1 DNA glyco-bond=s-- sugar=--- nts=3 GGG A.DG1,B.DG11,B.DG12
  strand#2 DNA glyco-bond=--- sugar=--- nts=3 GGG B.DG7,B.DG8,B.DG9
  strand#3 DNA glyco-bond=s-- sugar=--- nts=3 GGG B.DG1,A.DG11,A.DG12
  strand#4 DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG7,A.DG8,A.DG9

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2 stacking diagrams
 1  glyco-bond=s-s- sugar=---- groove=wnwn Major-->WC nts=4 GGGG A.DG1,B.DG7,B.DG1,A.DG7
2 glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG B.DG11,B.DG8,A.DG11,A.DG8
step#1 pm(>>,forward) area=8.84 rise=3.42 twist=32.4

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 2  glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG B.DG11,B.DG8,A.DG11,A.DG8
3 glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG B.DG12,B.DG9,A.DG12,A.DG9
step#2 pm(>>,forward) area=14.11 rise=3.40 twist=24.8

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

 1  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG8,A.DG11,B.DG8,B.DG11
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG9,A.DG12,B.DG9,B.DG12
  step#1  pm(>>,forward)  area=14.11 rise=3.40 twist=24.8
  strand#1  U DNA glyco-bond=-- sugar=-- nts=2 GG A.DG8,A.DG9
  strand#2  U DNA glyco-bond=-- sugar=-- nts=2 GG A.DG11,A.DG12
  strand#3  U DNA glyco-bond=-- sugar=-- nts=2 GG B.DG8,B.DG9
  strand#4  U DNA glyco-bond=-- sugar=-- nts=2 GG B.DG11,B.DG12
  loop#1 type=propeller strands=[#1,#2] nts=1 A A.DA10
  loop#2 type=propeller strands=[#3,#4] nts=1 A B.DA10

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List of 2 non-stem G4-loops (including the two closing Gs)

 1 type=lateral   helix=#1 nts=7 GCGGAGG A.DG1,A.DC2,A.DG3,A.DG4,A.DA5,A.DG6,A.DG7
 2 type=lateral   helix=#1 nts=7 GCGGAGG B.DG1,B.DC2,B.DG3,B.DG4,B.DA5,B.DG6,B.DG7