Detailed DSSR results for the G-quadruplex: PDB entry 2m27
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
- 2m27
- Class
- DNA
- Method
- NMR
- Summary
- Major g-quadruplex structure formed in human vegf promoter, a monomeric parallel-stranded quadruplex
- Reference
- Agrawal P, Hatzakis E, Guo K, Carver M, Yang D (2013): "Solution structure of the major G-quadruplex formed in the human VEGF promoter in K+: insights into loop interactions of the parallel G-quadruplexes." Nucleic Acids Res., 41, 10584-10592. doi: 10.1093/nar/gkt784.
- Abstract
- Vascular endothelial growth factor (VEGF) proximal promoter region contains a poly G/C-rich element that is essential for basal and inducible VEGF expression. The guanine-rich strand on this tract has been shown to form the DNA G-quadruplex structure, whose stabilization by small molecules can suppress VEGF expression. We report here the nuclear magnetic resonance structure of the major intramolecular G-quadruplex formed in this region in K(+) solution using the 22mer VEGF promoter sequence with G-to-T mutations of two loop residues. Our results have unambiguously demonstrated that the major G-quadruplex formed in the VEGF promoter in K(+) solution is a parallel-stranded structure with a 1:4:1 loop-size arrangement. A unique capping structure was shown to form in this 1:4:1 G-quadruplex. Parallel-stranded G-quadruplexes are commonly found in the human promoter sequences. The nuclear magnetic resonance structure of the major VEGF G-quadruplex shows that the 4-nt middle loop plays a central role for the specific capping structures and in stabilizing the most favored folding pattern. It is thus suggested that each parallel G-quadruplex likely adopts unique capping and loop structures by the specific middle loops and flanking segments, which together determine the overall structure and specific recognition sites of small molecules or proteins.LAY SUMMARY: The human VEGF is a key regulator of angiogenesis and plays an important role in tumor survival, growth and metastasis. VEGF overexpression is frequently found in a wide range of human tumors; the VEGF pathway has become an attractive target for cancer therapeutics. DNA G-quadruplexes have been shown to form in the proximal promoter region of VEGF and are amenable to small molecule drug targeting for VEGF suppression. The detailed molecular structure of the major VEGF promoter G-quadruplex reported here will provide an important basis for structure-based rational development of small molecule drugs targeting the VEGF G-quadruplex for gene suppression.
- 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=0.062 type=planar nts=4 GGGG A.DG3,A.DG7,A.DG14,A.DG18 2 glyco-bond=---- sugar=.... groove=---- planarity=0.032 type=planar nts=4 GGGG A.DG4,A.DG8,A.DG15,A.DG19 3 glyco-bond=---- sugar=.... groove=---- planarity=0.089 type=planar nts=4 GGGG A.DG5,A.DG9,A.DG16,A.DG20
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.DG7,A.DG14,A.DG18 2 glyco-bond=---- sugar=.... groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG8,A.DG15,A.DG19 3 glyco-bond=---- sugar=.... groove=---- WC-->Major nts=4 GGGG A.DG5,A.DG9,A.DG16,A.DG20 step#1 pm(>>,forward) area=19.04 rise=3.68 twist=22.8 step#2 pm(>>,forward) area=12.12 rise=3.75 twist=27.8 strand#1 DNA glyco-bond=--- sugar=... nts=3 GGG A.DG3,A.DG4,A.DG5 strand#2 DNA glyco-bond=--- sugar=... nts=3 GGG A.DG7,A.DG8,A.DG9 strand#3 DNA glyco-bond=--- sugar=... nts=3 GGG A.DG14,A.DG15,A.DG16 strand#4 DNA glyco-bond=--- sugar=... nts=3 GGG A.DG18,A.DG19,A.DG20 |
| 2 stacking diagrams | |
 |
1 glyco-bond=---- sugar=.... groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG7,A.DG14,A.DG18 |
 |
2 glyco-bond=---- sugar=.... groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG8,A.DG15,A.DG19 |
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.DG7,A.DG14,A.DG18 2 glyco-bond=---- sugar=.... groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG8,A.DG15,A.DG19 3 glyco-bond=---- sugar=.... groove=---- WC-->Major nts=4 GGGG A.DG5,A.DG9,A.DG16,A.DG20 step#1 pm(>>,forward) area=19.04 rise=3.68 twist=22.8 step#2 pm(>>,forward) area=12.12 rise=3.75 twist=27.8 strand#1 U DNA glyco-bond=--- sugar=... nts=3 GGG A.DG3,A.DG4,A.DG5 strand#2 U DNA glyco-bond=--- sugar=... nts=3 GGG A.DG7,A.DG8,A.DG9 strand#3 U DNA glyco-bond=--- sugar=... nts=3 GGG A.DG14,A.DG15,A.DG16 strand#4 U DNA glyco-bond=--- sugar=... nts=3 GGG A.DG18,A.DG19,A.DG20 loop#1 type=propeller strands=[#1,#2] nts=1 C A.DC6 loop#2 type=propeller strands=[#2,#3] nts=4 CCTT A.DC10,A.DC11,A.DT12,A.DT13 loop#3 type=propeller strands=[#3,#4] nts=1 C A.DC17 |