Detailed DSSR results for the G-quadruplex: PDB entry 7euc
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
- 7euc
- Class
- DNA
- Method
- NMR
- Summary
- Parallel g-quadruplex structure
- Reference
- Devi G, Winnerdy FR, Ang JCY, Lim KW, Phan AT (2022): "Four-Layered Intramolecular Parallel G-Quadruplex with Non-Nucleotide Loops: An Ultra-Stable Self-Folded DNA Nano-Scaffold." Acs Nano, 16, 533-540. doi: 10.1021/acsnano.1c07630.
- Abstract
- A four-stranded scaffold of nucleic acids termed G-quadruplex (G4) has found growing applications in nano- and biotechnology. Propeller loops are a hallmark of the most stable intramolecular parallel-stranded G4s. To date, propeller loops have been observed to span only a maximum of three G-tetrad layers. Going beyond that would allow creation of more stable scaffolds useful for building robust nanodevices. Here we investigate the formation of propeller loops spanning more than three layers. We show that native nucleotide sequences are incompatible toward this goal, and we report on synthetic non-nucleotide linkers that form a propeller loop across four layers. With the established linkers, we constructed a four-layered intramolecular parallel-stranded G4, which exhibited ultrahigh thermal stability. Control on loop design would augment the toolbox toward engineering of G4-based nanoscaffolds for diverse applications.
- G4 notes
- 4 G-tetrads, 1 G4 helix, 1 G4 stem, parallel(4+0), UUUU
Base-block schematics in six views
List of 4 G-tetrads
1 glyco-bond=---- sugar=-.-- groove=---- planarity=0.135 type=planar nts=4 GGGG A.DG3,B.DG9,C.DG15,D.DG21 2 glyco-bond=---- sugar=---- groove=---- planarity=0.087 type=planar nts=4 GGGG A.DG4,B.DG10,C.DG16,D.DG22 3 glyco-bond=---- sugar=---- groove=---- planarity=0.100 type=planar nts=4 GGGG A.DG5,B.DG11,C.DG17,D.DG23 4 glyco-bond=---- sugar=---- groove=---- planarity=0.076 type=planar nts=4 GGGG A.DG6,B.DG12,C.DG18,D.DG24
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, 4 G-tetrad layers, inter-molecular, with 1 stem
 |
1 glyco-bond=---- sugar=-.-- groove=---- WC-->Major nts=4 GGGG A.DG3,B.DG9,C.DG15,D.DG21 2 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG4,B.DG10,C.DG16,D.DG22 3 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG5,B.DG11,C.DG17,D.DG23 4 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG6,B.DG12,C.DG18,D.DG24 step#1 pm(>>,forward) area=9.07 rise=4.06 twist=29.5 step#2 pm(>>,forward) area=12.12 rise=3.59 twist=29.9 step#3 pm(>>,forward) area=13.25 rise=3.63 twist=30.9 strand#1 DNA glyco-bond=---- sugar=---- nts=4 GGGG A.DG3,A.DG4,A.DG5,A.DG6 strand#2 DNA glyco-bond=---- sugar=.--- nts=4 GGGG B.DG9,B.DG10,B.DG11,B.DG12 strand#3 DNA glyco-bond=---- sugar=---- nts=4 GGGG C.DG15,C.DG16,C.DG17,C.DG18 strand#4 DNA glyco-bond=---- sugar=---- nts=4 GGGG D.DG21,D.DG22,D.DG23,D.DG24 |
| 3 stacking diagrams | |
 |
1 glyco-bond=---- sugar=-.-- groove=---- WC-->Major nts=4 GGGG A.DG3,B.DG9,C.DG15,D.DG21 |
 |
2 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG4,B.DG10,C.DG16,D.DG22 |
 |
3 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG5,B.DG11,C.DG17,D.DG23 |
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, 4 G-tetrad layers, 0 loops, inter-molecular, UUUU, parallel, parallel(4+0)
 |
1 glyco-bond=---- sugar=-.-- groove=---- WC-->Major nts=4 GGGG A.DG3,B.DG9,C.DG15,D.DG21 2 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG4,B.DG10,C.DG16,D.DG22 3 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG5,B.DG11,C.DG17,D.DG23 4 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG6,B.DG12,C.DG18,D.DG24 step#1 pm(>>,forward) area=9.07 rise=4.06 twist=29.5 step#2 pm(>>,forward) area=12.12 rise=3.59 twist=29.9 step#3 pm(>>,forward) area=13.25 rise=3.63 twist=30.9 strand#1 U DNA glyco-bond=---- sugar=---- nts=4 GGGG A.DG3,A.DG4,A.DG5,A.DG6 strand#2 U DNA glyco-bond=---- sugar=.--- nts=4 GGGG B.DG9,B.DG10,B.DG11,B.DG12 strand#3 U DNA glyco-bond=---- sugar=---- nts=4 GGGG C.DG15,C.DG16,C.DG17,C.DG18 strand#4 U DNA glyco-bond=---- sugar=---- nts=4 GGGG D.DG21,D.DG22,D.DG23,D.DG24 |