Detailed DSSR results for the G-quadruplex: PDB entry 7cls
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
- 7cls
- Class
- DNA
- Method
- NMR
- Summary
- Solution structure of an intramolecular g-quadruplex containing a duplex bulge
- Reference
- Ngoc Nguyen TQ, Lim KW, Phan AT (2020): "Duplex formation in a G-quadruplex bulge." Nucleic Acids Res., 48, 10567-10575. doi: 10.1093/nar/gkaa738.
- Abstract
- Beyond the consensus definition of G-quadruplex-forming motifs with tracts of continuous guanines, G-quadruplexes harboring bulges in the G-tetrad core are prevalent in the human genome. Here, we study the incorporation of a duplex hairpin within a bulge of a G-quadruplex. The NMR solution structure of a G-quadruplex containing a duplex bulge was resolved, revealing the structural details of the junction between the duplex bulge and the G-quadruplex. Unexpectedly, instead of an orthogonal connection the duplex stem was observed to stack below the G-quadruplex forming a unique quadruplex-duplex junction. Breaking up of the immediate base pair step at the junction, coupled with a narrowing of the duplex groove within the context of the bulge, led to a progressive transition between the quadruplex and duplex segments. This study revealed that a duplex bulge can be formed at various positions of a G-quadruplex scaffold. In contrast to a non-structured bulge, the stability of a G-quadruplex slightly increases with an increase in the duplex bulge size. A G-quadruplex structure containing a duplex bulge of up to 33 nt in size was shown to form, which was much larger than the previously reported 7-nt bulge. With G-quadruplexes containing duplex bulges representing new structural motifs with potential biological significance, our findings would broaden the definition of potential G-quadruplex-forming sequences.
- G4 notes
- 3 G-tetrads, 1 G4 helix, 1 G4 stem, 3(-P-P-P), parallel(4+0), UUUU
Base-block schematics in six views
List of 3 G-tetrads
1 glyco-bond=---- sugar=-.-- groove=---- planarity=0.138 type=planar nts=4 GGGG A.DG3,A.DG22,A.DG26,A.DG30 2 glyco-bond=---- sugar=---- groove=---- planarity=0.096 type=planar nts=4 GGGG A.DG4,A.DG23,A.DG27,A.DG31 3 glyco-bond=s--- sugar=---- groove=w--n planarity=0.101 type=planar nts=4 GGGG A.DG20,A.DG32,A.DG28,A.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, 3 G-tetrad layers, INTRA-molecular, with 1 stem
 |
1 glyco-bond=---- sugar=-.-- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG22,A.DG26,A.DG30 2 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG23,A.DG27,A.DG31 3 glyco-bond=s--- sugar=---- groove=n--w WC-->Major nts=4 GGGG A.DG20,A.DG24,A.DG28,A.DG32 step#1 pm(>>,forward) area=12.31 rise=3.39 twist=30.2 step#2 pm(>>,forward) area=11.25 rise=3.39 twist=31.6 strand#1 DNA glyco-bond=--s sugar=--- nts=3 GGG A.DG3,A.DG4,A.DG20 strand#2 DNA glyco-bond=--- sugar=.-- nts=3 GGG A.DG22,A.DG23,A.DG24 strand#3 DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG26,A.DG27,A.DG28 strand#4 DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG30,A.DG31,A.DG32 |
| 2 stacking diagrams | |
 |
1 glyco-bond=---- sugar=-.-- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG22,A.DG26,A.DG30 |
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2 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG23,A.DG27,A.DG31 |
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, UUUU, parallel, 3(-P-P-P), parallel(4+0)
 |
1 glyco-bond=---- sugar=-.-- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG22,A.DG26,A.DG30 2 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG23,A.DG27,A.DG31 3 glyco-bond=s--- sugar=---- groove=n--w WC-->Major nts=4 GGGG A.DG20,A.DG24,A.DG28,A.DG32 step#1 pm(>>,forward) area=12.31 rise=3.39 twist=30.2 step#2 pm(>>,forward) area=11.25 rise=3.39 twist=31.6 strand#1* U DNA glyco-bond=--s sugar=--- nts=3 GGG A.DG3,A.DG4,A.DG20 bulged-nts=15 ATCTGAGAATCAGAT A.DA5,A.DT6,A.DC7,A.DT8,A.DG9,A.DA10,A.DG11,A.DA12,A.DA13,A.DT14,A.DC15,A.DA16,A.DG17,A.DA18,A.DT19 strand#2 U DNA glyco-bond=--- sugar=.-- nts=3 GGG A.DG22,A.DG23,A.DG24 strand#3 U DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG26,A.DG27,A.DG28 strand#4 U DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG30,A.DG31,A.DG32 loop#1 type=propeller strands=[#1,#2] nts=1 T A.DT21 loop#2 type=propeller strands=[#2,#3] nts=1 T A.DT25 loop#3 type=propeller strands=[#3,#4] nts=1 T A.DT29 |