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

PDB-id
6sx6
Class
DNA
Method
NMR
Summary
Guanine-rich oligonucleotide with 5'-gc end form G-quadruplex with a(gggg)a hexad, gcgc- and G-quartets and two symmetric gg and aa base pairs
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.
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 [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=s-s- groove=wnwn planarity=0.331 type=other  nts=4 GGGG A.DG1,B.DG7,B.DG1,A.DG7
 2 glyco-bond=---- groove=---- planarity=0.190 type=other  nts=4 GGGG A.DG8,A.DG11,B.DG8,B.DG11
 3 glyco-bond=---- groove=---- planarity=0.150 type=planar nts=4 GGGG A.DG9,A.DG12,B.DG9,B.DG12

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, inter-molecular, with 1 stem

 1  glyco-bond=s-s- groove=wnwn Major-->WC nts=4 GGGG A.DG1,B.DG7,B.DG1,A.DG7
 2  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG B.DG11,B.DG8,A.DG11,A.DG8
 3  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG B.DG12,B.DG9,A.DG12,A.DG9
  step#1  pm(>>,forward)  area=9.35  rise=3.34 twist=34.0
  step#2  pm(>>,forward)  area=10.34 rise=3.43 twist=29.1
  strand#1 DNA glyco-bond=s-- nts=3 GGG A.DG1,B.DG11,B.DG12
  strand#2 DNA glyco-bond=--- nts=3 GGG B.DG7,B.DG8,B.DG9
  strand#3 DNA glyco-bond=s-- nts=3 GGG B.DG1,A.DG11,A.DG12
  strand#4 DNA glyco-bond=--- nts=3 GGG A.DG7,A.DG8,A.DG9

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2 stacking diagrams
 1  glyco-bond=s-s- groove=wnwn Major-->WC nts=4 GGGG A.DG1,B.DG7,B.DG1,A.DG7
2 glyco-bond=---- groove=---- Major-->WC nts=4 GGGG B.DG11,B.DG8,A.DG11,A.DG8
step#1 pm(>>,forward) area=9.35 rise=3.34 twist=34.0

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 2  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG B.DG11,B.DG8,A.DG11,A.DG8
3 glyco-bond=---- groove=---- Major-->WC nts=4 GGGG B.DG12,B.DG9,A.DG12,A.DG9
step#2 pm(>>,forward) area=10.34 rise=3.43 twist=29.1

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

 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG8,A.DG11,B.DG8,B.DG11
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG9,A.DG12,B.DG9,B.DG12
  step#1  pm(>>,forward)  area=10.34 rise=3.43 twist=29.1
  strand#1  U DNA glyco-bond=-- nts=2 GG A.DG8,A.DG9
  strand#2  U DNA glyco-bond=-- nts=2 GG A.DG11,A.DG12
  strand#3  U DNA glyco-bond=-- nts=2 GG B.DG8,B.DG9
  strand#4  U DNA glyco-bond=-- 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 0 G4 coaxial stacks [summary · schematics · tetrads · helices · stems · homepage]

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