DSSR-enabled G4 identification/annotation: PDB entry 2m1g
Summary information and primary citation
- PDB-id
- 2m1g
- Class
- DNA
- Method
- NMR
- Summary
- Parallel human telomeric quadruplex containing 2'f-ana substitutions
- Reference
- Martin-Pintado N, Yahyaee-Anzahaee M, Deleavey GF, Portella G, Orozco M, Damha MJ, Gonzalez C (2013): "Dramatic effect of furanose c2' substitution on structure and stability: directing the folding of the human telomeric quadruplex with a single fluorine atom." J.Am.Chem.Soc., 135, 5344-5347. doi: 10.1021/ja401954t.
- Abstract
- Human telomeric DNA quadruplexes can adopt different conformations in solution. We have found that arabinose, 2'F-arabinose, and ribose substitutions stabilize the propeller parallel G-quadruplex form over competing conformers, allowing NMR structural determination of this particularly significant nucleic acid structure. 2'F-arabinose substitution provides the greatest stabilization as a result of electrostatic (F-CH---O4') and pseudo-hydrogen-bond (F---H8) stabilizing interactions. In contrast, 2'F-rG substitution provokes a dramatic destabilization of the quadruplex structure due to unfavorable electrostatic repulsion between the phosphate and the 2'-F.
- G4 notes
- 3 G-tetrads, 1 G4 helix, 1 G4 stem, UUUU, parallel, 4+0
Cartoon-block schematics in six views (download the tarball)
List of 3 G-tetrads
1 glyco-bond=---- sugar=---- groove=---- planarity=0.336 type=other -- nts=4 GgGg A.DG3,A.GFL9,B.DG15,B.GFL21 2 glyco-bond=---- sugar=---- groove=---- planarity=0.143 type=planar -- nts=4 GGGG A.DG4,A.DG10,B.DG16,B.DG22 3 glyco-bond=---- sugar=---- groove=---- planarity=0.367 type=bowl -- nts=4 GGGG A.DG5,A.DG11,B.DG17,B.DG23
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-tetrads, inter-molecular, with 1 stem
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1 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GgGg A.DG3,A.GFL9,B.DG15,B.GFL21 2 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG A.DG4,A.DG10,B.DG16,B.DG22 3 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG A.DG5,A.DG11,B.DG17,B.DG23 step#1 pm(>>,forward) area=18.09 rise=3.47 twist=20.8 step#2 pm(>>,forward) area=11.88 rise=3.58 twist=25.1 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.GFL9,A.DG10,A.DG11 strand#3 DNA glyco-bond=--- sugar=--- nts=3 GGG B.DG15,B.DG16,B.DG17 strand#4 DNA glyco-bond=--- sugar=--- nts=3 gGG B.GFL21,B.DG22,B.DG23 |
| 2 stacking diagrams | |
|
1 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GgGg A.DG3,A.GFL9,B.DG15,B.GFL21 |
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2 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG A.DG4,A.DG10,B.DG16,B.DG22 |
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-tetrads, 2 loops, inter-molecular, UUUU, parallel, 4+0
|
1 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GgGg A.DG3,A.GFL9,B.DG15,B.GFL21 2 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG A.DG4,A.DG10,B.DG16,B.DG22 3 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG A.DG5,A.DG11,B.DG17,B.DG23 step#1 pm(>>,forward) area=18.09 rise=3.47 twist=20.8 step#2 pm(>>,forward) area=11.88 rise=3.58 twist=25.1 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.GFL9,A.DG10,A.DG11 strand#3 U DNA glyco-bond=--- sugar=--- nts=3 GGG B.DG15,B.DG16,B.DG17 strand#4 U DNA glyco-bond=--- sugar=--- nts=3 gGG B.GFL21,B.DG22,B.DG23 loop#1 type=propeller strands=[#1,#2] nts=3 TTA A.DT6,A.DT7,A.DA8 loop#2 type=propeller strands=[#3,#4] nts=3 TTA B.DT18,B.DT19,B.DA20 |