Detailed DSSR results for the G-quadruplex: PDB entry 2m53
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
- 2m53
- Class
- DNA
- Method
- NMR
- Summary
- G-rich vegf aptamer with lna modifications
- Reference
- Marusic M, Veedu RN, Wengel J, Plavec J (2013): "G-rich VEGF aptamer with locked and unlocked nucleic acid modifications exhibits a unique G-quadruplex fold." Nucleic Acids Res., 41, 9524-9536. doi: 10.1093/nar/gkt697.
- Abstract
- The formation of a single G-quadruplex structure adopted by a promising 25 nt G-rich vascular endothelial growth factor aptamer in a K(+) rich environment was facilitated by locked nucleic acid modifications. An unprecedented all parallel-stranded monomeric G-quadruplex with three G-quartet planes exhibits several unique structural features. Five consecutive guanine residues are all involved in G-quartet formation and occupy positions in adjacent DNA strands, which are bridged with a no-residue propeller-type loop. A two-residue D-shaped loop facilitates inclusion of an isolated guanine residue into the vacant spot within the G-quartet. The remaining two G-rich tracts of three residues each adopt parallel orientation and are linked with edgewise and propeller loops. Both 5' with 3 nt and 3' with 4 nt overhangs display well-defined conformations, with latter adopting a basket handle topology. Locked residues contribute to thermal stabilization of the adopted structure and formation of structurally pre-organized intermediates that facilitate folding into a single G-quadruplex. Understanding the impact of chemical modifications on folding, thermal stability and structural polymorphism of G-quadruplexes provides means for the improvement of vascular endothelial growth factor aptamers and advances our insights into driving nucleic acid structure by locking or unlocking the conformation of sugar moieties of nucleotides in general.
- G4 notes
- 3 G-tetrads, 1 G4 helix, 1 G4 stem, 2(-P-P-P), parallel(4+0), UUUU
Base-block schematics in six views
List of 3 G-tetrads
1 glyco-bond=---- sugar=3-.3 groove=---- planarity=0.352 type=other nts=4 GGGG A.DG4,A.DG11,A.DG14,A.DG19 2 glyco-bond=---- sugar=3.-. groove=---- planarity=0.174 type=other nts=4 gGGG A.LCG5,A.DG7,A.DG15,A.DG20 3 glyco-bond=---- sugar=---3 groove=---- planarity=0.200 type=other nts=4 GGGg A.DG6,A.DG8,A.DG16,A.LCG21
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=3-.3 groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG11,A.DG14,A.DG19 2 glyco-bond=---- sugar=3.-. groove=---- WC-->Major nts=4 gGGG A.LCG5,A.DG7,A.DG15,A.DG20 3 glyco-bond=---- sugar=---3 groove=---- WC-->Major nts=4 GGGg A.DG6,A.DG8,A.DG16,A.LCG21 step#1 pm(>>,forward) area=24.23 rise=3.66 twist=11.9 step#2 pm(>>,forward) area=13.48 rise=3.32 twist=26.7 strand#1 DNA glyco-bond=--- sugar=33- nts=3 GgG A.DG4,A.LCG5,A.DG6 strand#2 DNA glyco-bond=--- sugar=-.- nts=3 GGG A.DG11,A.DG7,A.DG8 strand#3 DNA glyco-bond=--- sugar=.-- nts=3 GGG A.DG14,A.DG15,A.DG16 strand#4 DNA glyco-bond=--- sugar=3.3 nts=3 GGg A.DG19,A.DG20,A.LCG21 |
| 2 stacking diagrams | |
 |
1 glyco-bond=---- sugar=3-.3 groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG11,A.DG14,A.DG19 |
 |
2 glyco-bond=---- sugar=3.-. groove=---- WC-->Major nts=4 gGGG A.LCG5,A.DG7,A.DG15,A.DG20 |
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, 2 G-tetrad layers, 3 loops, INTRA-molecular, UUUU, parallel, 2(-P-P-P), parallel(4+0)
 |
1 glyco-bond=---- sugar=3.-. groove=---- WC-->Major nts=4 gGGG A.LCG5,A.DG7,A.DG15,A.DG20 2 glyco-bond=---- sugar=---3 groove=---- WC-->Major nts=4 GGGg A.DG6,A.DG8,A.DG16,A.LCG21 step#1 pm(>>,forward) area=13.48 rise=3.32 twist=26.7 strand#1 U DNA glyco-bond=-- sugar=3- nts=2 gG A.LCG5,A.DG6 strand#2 U DNA glyco-bond=-- sugar=.- nts=2 GG A.DG7,A.DG8 strand#3 U DNA glyco-bond=-- sugar=-- nts=2 GG A.DG15,A.DG16 strand#4 U DNA glyco-bond=-- sugar=.3 nts=2 Gg A.DG20,A.LCG21 loop#1 type=propeller strands=[#1,#2] nts=0 loop#2 type=propeller strands=[#2,#3] nts=6 TGGACG A.DT9,A.DG10,A.DG11,A.DA12,A.DC13,A.DG14 loop#3 type=propeller strands=[#3,#4] nts=3 CCG A.DC17,A.DC18,A.DG19 |
List of 1 non-stem G4-loop (including the two closing Gs)
1 type=lateral helix=#1 nts=4 GACG A.DG11,A.DA12,A.DC13,A.DG14