Summary information

PDB id
8qkx
Class
DNA
Method
NMR
Summary
Solution structure of a bimolecular quadruplex-duplex hybrid containing a v-shaped loop
Reference
Agustin DF, Vianney YM, Weisz K, Wahjudi M (2024): "Structural Aspects of Split G-Quadruplexes in Quadruplex-Duplex Hybrid Systems." Chemistryselect. doi: 10.1002/slct.202304286.
Abstract
 
G4 notes
3 G-tetrads, 1 G4 helix, 1 G4 stem, (3+1), UDUU

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=--3- groove=w-n- planarity=0.162 type=other  nts=4 GGGG A.DG9,B.DG28,A.DG16,A.DG21
 2 glyco-bond=-s-- sugar=---- groove=wn-- planarity=0.150 type=planar nts=4 GGGG A.DG10,B.DG27,A.DG17,A.DG22
 3 glyco-bond=-s-- sugar=-3-- groove=wn-- planarity=0.272 type=other  nts=4 GGGG A.DG11,A.DG15,A.DG18,A.DG23

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=--3- groove=w-n- Major-->WC nts=4 GGGG A.DG9,B.DG28,A.DG16,A.DG21
 2  glyco-bond=-s-- sugar=---- groove=wn-- WC-->Major nts=4 GGGG A.DG10,B.DG27,A.DG17,A.DG22
 3  glyco-bond=-s-- sugar=-3-- groove=wn-- WC-->Major nts=4 GGGG A.DG11,A.DG15,A.DG18,A.DG23
  step#1  mm(<>,outward)  area=7.29  rise=3.39 twist=27.7
  step#2  pm(>>,forward)  area=15.30 rise=3.51 twist=22.6
  strand#1 DNA glyco-bond=s-- sugar=--- nts=3 GGG A.DG9,A.DG10,A.DG11
  strand#2 DNA glyco-bond=-ss sugar=--3 nts=3 GGG B.DG28,B.DG27,A.DG15
  strand#3 DNA glyco-bond=--- sugar=3-- nts=3 GGG A.DG16,A.DG17,A.DG18
  strand#4 DNA glyco-bond=s-- sugar=--- nts=3 GGG A.DG21,A.DG22,A.DG23

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2 stacking diagrams 
 1  glyco-bond=s--s sugar=--3- groove=w-n- Major-->WC nts=4 GGGG A.DG9,B.DG28,A.DG16,A.DG21
 2  glyco-bond=-s-- sugar=---- groove=wn-- WC-->Major nts=4 GGGG A.DG10,B.DG27,A.DG17,A.DG22
  step#1  mm(<>,outward)  area=7.29  rise=3.39 twist=27.7

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 2  glyco-bond=-s-- sugar=---- groove=wn-- WC-->Major nts=4 GGGG A.DG10,B.DG27,A.DG17,A.DG22
 3  glyco-bond=-s-- sugar=-3-- groove=wn-- WC-->Major nts=4 GGGG A.DG11,A.DG15,A.DG18,A.DG23
  step#2  pm(>>,forward)  area=15.30 rise=3.51 twist=22.6

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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, UDUU, hybrid-(mixed), (3+1)

 1  glyco-bond=s--s sugar=--3- groove=w-n- Major-->WC nts=4 GGGG A.DG9,B.DG28,A.DG16,A.DG21
 2  glyco-bond=-s-- sugar=---- groove=wn-- WC-->Major nts=4 GGGG A.DG10,B.DG27,A.DG17,A.DG22
  step#1  mm(<>,outward)  area=7.29  rise=3.39 twist=27.7
  strand#1  U DNA glyco-bond=s- sugar=-- nts=2 GG A.DG9,A.DG10
  strand#2  D DNA glyco-bond=-s sugar=-- nts=2 GG B.DG28,B.DG27
  strand#3  U DNA glyco-bond=-- sugar=3- nts=2 GG A.DG16,A.DG17
  strand#4  U DNA glyco-bond=s- sugar=-- nts=2 GG A.DG21,A.DG22
  loop#1 type=diag-prop strands=[#1,#3] nts=5 GTGAG A.DG11,A.DT12,A.DG13,A.DA14,A.DG15
  loop#2 type=propeller strands=[#3,#4] nts=3 GCT A.DG18,A.DC19,A.DT20

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

 1 type=lateral   helix=#1 nts=5 GTGAG A.DG11,A.DT12,A.DG13,A.DA14,A.DG15
 2 type=V-shaped  helix=#1 nts=4 GGGG A.DG15,A.DG16,A.DG17,A.DG18