Detailed DSSR results for the G-quadruplex: PDB entry 8s1w
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
- 8s1w
- Class
- DNA
- Method
- NMR
- Summary
- Structure of a quadruplex-duplex hybrid with a (-pd+l) loop progression
- Reference
- Vianney YM, Jana J, Weisz K (2024): "A pH-Responsive Topological Switch Based on a DNA Quadruplex-Duplex Hybrid." Chemistry, 30, e202400722. doi: 10.1002/chem.202400722.
- Abstract
- A guanine-rich oligonucleotide based on a human telomeric sequence but with the first three-nucleotide intervening stretch replaced by a putative 15-nucleotide hairpin-forming sequence shows a pH-dependent folding into different quadruplex-duplex hybrids in a potassium containing buffer. At slightly acidic pH, the quadruplex domain adopts a chair-type conformation. Upon increasing the pH, a transition with a midpoint close to neutral pH to a major and minor (3+1) hybrid topology with either a coaxially stacked or orthogonally oriented duplex stem-loop occurs. NMR-derived high-resolution structures reveal that an adenine protonation is prerequisite for the formation of a non-canonical base quartet, capping the outer G-tetrad at the quadruplex-duplex interface and stabilizing the antiparallel chair conformation in an acidic environment. Being directly associated with interactions at the quadruplex-duplex interface, this unique pH-dependent topological transition is fully reversible. Coupled with a conformation-sensitive optical readout demonstrated as a proof of concept using the fluorescent dye thiazole orange, the present quadruplex-duplex hybrid architecture represents a potentially valuable pH-sensing system responsive in a physiological pH range of 7±1.
- G4 notes
- 3 G-tetrads, 1 G4 helix, 1 G4 stem, 3(-PD+Lw), U3D(3+1), UUUD
Base-block schematics in six views
List of 3 G-tetrads
1 glyco-bond=sss- sugar=---- groove=--wn planarity=0.276 type=other nts=4 GGGG A.DG1,A.DG18,A.DG31,A.DG27 2 glyco-bond=---s sugar=---- groove=--wn planarity=0.359 type=other nts=4 GGGg A.DG2,A.DG19,A.DG32,A.BGM26 3 glyco-bond=---s sugar=.--- groove=--wn planarity=0.432 type=bowl nts=4 GGGG A.DG3,A.DG20,A.DG33,A.DG25
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=sss- sugar=---- groove=--wn Major-->WC nts=4 GGGG A.DG1,A.DG18,A.DG31,A.DG27 2 glyco-bond=---s sugar=---- groove=--wn WC-->Major nts=4 GGGg A.DG2,A.DG19,A.DG32,A.BGM26 3 glyco-bond=---s sugar=.--- groove=--wn WC-->Major nts=4 GGGG A.DG3,A.DG20,A.DG33,A.DG25 step#1 mm(<>,outward) area=15.56 rise=3.49 twist=18.0 step#2 pm(>>,forward) area=11.83 rise=3.59 twist=26.1 strand#1 DNA glyco-bond=s-- sugar=--. nts=3 GGG A.DG1,A.DG2,A.DG3 strand#2 DNA glyco-bond=s-- sugar=--- nts=3 GGG A.DG18,A.DG19,A.DG20 strand#3 DNA glyco-bond=s-- sugar=--- nts=3 GGG A.DG31,A.DG32,A.DG33 strand#4 DNA glyco-bond=-ss sugar=--- nts=3 GgG A.DG27,A.BGM26,A.DG25 |
| 2 stacking diagrams | |
 |
1 glyco-bond=sss- sugar=---- groove=--wn Major-->WC nts=4 GGGG A.DG1,A.DG18,A.DG31,A.DG27 |
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2 glyco-bond=---s sugar=---- groove=--wn WC-->Major nts=4 GGGg A.DG2,A.DG19,A.DG32,A.BGM26 |
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, UUUD, hybrid-(mixed), 3(-PD+Lw), U3D(3+1)
 |
1 glyco-bond=sss- sugar=---- groove=--wn Major-->WC nts=4 GGGG A.DG1,A.DG18,A.DG31,A.DG27 2 glyco-bond=---s sugar=---- groove=--wn WC-->Major nts=4 GGGg A.DG2,A.DG19,A.DG32,A.BGM26 3 glyco-bond=---s sugar=.--- groove=--wn WC-->Major nts=4 GGGG A.DG3,A.DG20,A.DG33,A.DG25 step#1 mm(<>,outward) area=15.56 rise=3.49 twist=18.0 step#2 pm(>>,forward) area=11.83 rise=3.59 twist=26.1 strand#1 U DNA glyco-bond=s-- sugar=--. nts=3 GGG A.DG1,A.DG2,A.DG3 strand#2 U DNA glyco-bond=s-- sugar=--- nts=3 GGG A.DG18,A.DG19,A.DG20 strand#3 U DNA glyco-bond=s-- sugar=--- nts=3 GGG A.DG31,A.DG32,A.DG33 strand#4 D DNA glyco-bond=-ss sugar=--- nts=3 GgG A.DG27,A.BGM26,A.DG25 loop#1 type=propeller strands=[#1,#2] nts=14 CGCGAAGCATTCGC 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 loop#2 type=diagonal strands=[#2,#4] nts=4 GTTA A.DG21,A.DT22,A.DT23,A.DA24 loop#3 type=lateral strands=[#4,#3] nts=3 TTA A.DT28,A.DT29,A.DA30 |