Summary information

PDB id
8r6g
Class
DNA
Method
NMR
Summary
A quadruplex-duplex hybrid with a three-layered chair g-quadruplex topology
Reference
Vianney YM, Dierks D, Weisz K (2024): "Structural Differences at Quadruplex-Duplex Interfaces Enable Ligand-Induced Topological Transitions." Adv Sci, e2309891. doi: 10.1002/advs.202309891.
Abstract
Quadruplex-duplex (QD) junctions, which represent unique structural motifs of both biological and technological significance, have been shown to constitute high-affinity binding sites for various ligands. A QD hybrid construct based on a human telomeric sequence, which harbors a duplex stem-loop in place of a short lateral loop, is structurally characterized by NMR. It folds into two major species with a (3+1) hybrid and a chair-type (2+2) antiparallel quadruplex domain coexisting in a K+ buffer solution. The antiparallel species is stabilized by an unusual capping structure involving a thymine and protonated adenine base AH+ of the lateral loop facing the hairpin duplex to form a T·AH+ ·G·C quartet with the interfacial G·C base pair at neutral pH. Addition and binding of Phen-DC3 to the QD hybrid mixture by its partial intercalation at corresponding QD junctions leads to a topological transition with exclusive formation of the (3+1) hybrid fold. In agreement with the available experimental data, such an unprecedented discrimination of QD junctions by a ligand can be rationalized following an induced fit mechanism.
G4 notes
3 G-tetrads, 1 G4 helix, 1 G4 stem, 3(-Lw-Ln-Lw), chair(2+2), UDUD

List of 3 G-tetrads

 1 glyco-bond=s-s- sugar=---- groove=wnwn planarity=0.418 type=bowl-2 nts=4 GGGG A.DG1,A.DG21,A.DG25,A.DG33
 2 glyco-bond=-s-s sugar=---- groove=wnwn planarity=0.309 type=saddle nts=4 GGGg A.DG2,A.DG20,A.DG26,A.BGM32
 3 glyco-bond=-s-s sugar=---- groove=wnwn planarity=0.243 type=other  nts=4 GGGG A.DG3,A.DG19,A.DG27,A.DG31

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, INTRA-molecular, with 1 stem

 1  glyco-bond=s-s- sugar=---- groove=wnwn Major-->WC nts=4 GGGG A.DG1,A.DG21,A.DG25,A.DG33
 2  glyco-bond=-s-s sugar=---- groove=wnwn WC-->Major nts=4 GGGg A.DG2,A.DG20,A.DG26,A.BGM32
 3  glyco-bond=-s-s sugar=---- groove=wnwn WC-->Major nts=4 GGGG A.DG3,A.DG19,A.DG27,A.DG31
  step#1  mm(<>,outward)  area=16.10 rise=3.49 twist=18.7
  step#2  pm(>>,forward)  area=13.83 rise=3.34 twist=28.0
  strand#1 DNA glyco-bond=s-- sugar=--- nts=3 GGG A.DG1,A.DG2,A.DG3
  strand#2 DNA glyco-bond=-ss sugar=--- nts=3 GGG A.DG21,A.DG20,A.DG19
  strand#3 DNA glyco-bond=s-- sugar=--- nts=3 GGG A.DG25,A.DG26,A.DG27
  strand#4 DNA glyco-bond=-ss sugar=--- nts=3 GgG A.DG33,A.BGM32,A.DG31

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2 stacking diagrams 
 1  glyco-bond=s-s- sugar=---- groove=wnwn Major-->WC nts=4 GGGG A.DG1,A.DG21,A.DG25,A.DG33
 2  glyco-bond=-s-s sugar=---- groove=wnwn WC-->Major nts=4 GGGg A.DG2,A.DG20,A.DG26,A.BGM32
  step#1  mm(<>,outward)  area=16.10 rise=3.49 twist=18.7

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 2  glyco-bond=-s-s sugar=---- groove=wnwn WC-->Major nts=4 GGGg A.DG2,A.DG20,A.DG26,A.BGM32
 3  glyco-bond=-s-s sugar=---- groove=wnwn WC-->Major nts=4 GGGG A.DG3,A.DG19,A.DG27,A.DG31
  step#2  pm(>>,forward)  area=13.83 rise=3.34 twist=28.0

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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, 3 G-tetrad layers, 3 loops, INTRA-molecular, UDUD, anti-parallel, 3(-Lw-Ln-Lw), chair(2+2)

 1  glyco-bond=s-s- sugar=---- groove=wnwn Major-->WC nts=4 GGGG A.DG1,A.DG21,A.DG25,A.DG33
 2  glyco-bond=-s-s sugar=---- groove=wnwn WC-->Major nts=4 GGGg A.DG2,A.DG20,A.DG26,A.BGM32
 3  glyco-bond=-s-s sugar=---- groove=wnwn WC-->Major nts=4 GGGG A.DG3,A.DG19,A.DG27,A.DG31
  step#1  mm(<>,outward)  area=16.10 rise=3.49 twist=18.7
  step#2  pm(>>,forward)  area=13.83 rise=3.34 twist=28.0
  strand#1  U DNA glyco-bond=s-- sugar=--- nts=3 GGG A.DG1,A.DG2,A.DG3
  strand#2  D DNA glyco-bond=-ss sugar=--- nts=3 GGG A.DG21,A.DG20,A.DG19
  strand#3  U DNA glyco-bond=s-- sugar=--- nts=3 GGG A.DG25,A.DG26,A.DG27
  strand#4  D DNA glyco-bond=-ss sugar=--- nts=3 GgG A.DG33,A.BGM32,A.DG31
  loop#1 type=lateral   strands=[#1,#2] nts=15 CGCGAAGCATTCGCG A.DC4,A.DG5,A.DC6,A.DG7,A.DA8,A.DA9,A.DG10,A.DC11,A.DA12,A.DT13,A.DT14,A.DC15,A.DG16,A.DC17,A.DG18
  loop#2 type=lateral   strands=[#2,#3] nts=3 TTA A.DT22,A.DT23,A.DA24
  loop#3 type=lateral   strands=[#3,#4] nts=3 TTa A.DT28,A.DT29,A.A1H30

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