Detailed DSSR results for the G-quadruplex: PDB entry 8r6d
Created and maintained by Xiang-Jun Lu <xiangjun@x3dna.org>
Citation: Please cite the NAR'20 DSSR-PyMOL schematics paper and/or the NAR'15 DSSR method paper.
Summary information
- PDB id
- 8r6d
- Class
- DNA
- Method
- NMR
- Summary
- A quadruplex-duplex hybrid with a three-layered hybrid-2 g-quadruplex topology
- Reference
- Vianney YM, Dierks D, Weisz K (2024): "Structural Differences at Quadruplex-Duplex Interfaces Enable Ligand-Induced Topological Transitions." Adv Sci, 11, 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-P), hybrid-2(3+1), UDUU
Base-block schematics in six views
List of 3 G-tetrads
1 glyco-bond=s-ss sugar=---- groove=wn-- planarity=0.131 type=planar nts=4 GGGG A.DG1,A.DG21,A.DG25,A.DG29 2 glyco-bond=-s-- sugar=---- groove=wn-- planarity=0.094 type=planar nts=4 GGGG A.DG2,A.DG20,A.DG26,A.DG30 3 glyco-bond=-s-- sugar=---- groove=wn-- planarity=0.123 type=planar 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-ss sugar=---- groove=wn-- Major-->WC nts=4 GGGG A.DG1,A.DG21,A.DG25,A.DG29 2 glyco-bond=-s-- sugar=---- groove=wn-- WC-->Major nts=4 GGGG A.DG2,A.DG20,A.DG26,A.DG30 3 glyco-bond=-s-- sugar=---- groove=wn-- WC-->Major nts=4 GGGG A.DG3,A.DG19,A.DG27,A.DG31 step#1 mm(<>,outward) area=14.25 rise=3.43 twist=19.7 step#2 pm(>>,forward) area=10.80 rise=3.44 twist=29.5 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=s-- sugar=--- nts=3 GGG A.DG29,A.DG30,A.DG31 |
| 2 stacking diagrams | |
 |
1 glyco-bond=s-ss sugar=---- groove=wn-- Major-->WC nts=4 GGGG A.DG1,A.DG21,A.DG25,A.DG29 |
 |
2 glyco-bond=-s-- sugar=---- groove=wn-- WC-->Major nts=4 GGGG A.DG2,A.DG20,A.DG26,A.DG30 |
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, UDUU, hybrid-(mixed), 3(-Lw-Ln-P), hybrid-2(3+1)
 |
1 glyco-bond=s-ss sugar=---- groove=wn-- Major-->WC nts=4 GGGG A.DG1,A.DG21,A.DG25,A.DG29 2 glyco-bond=-s-- sugar=---- groove=wn-- WC-->Major nts=4 GGGG A.DG2,A.DG20,A.DG26,A.DG30 3 glyco-bond=-s-- sugar=---- groove=wn-- WC-->Major nts=4 GGGG A.DG3,A.DG19,A.DG27,A.DG31 step#1 mm(<>,outward) area=14.25 rise=3.43 twist=19.7 step#2 pm(>>,forward) area=10.80 rise=3.44 twist=29.5 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 U DNA glyco-bond=s-- sugar=--- nts=3 GGG A.DG29,A.DG30,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=propeller strands=[#3,#4] nts=1 T A.DT28 |