Detailed DSSR results for the G-quadruplex: PDB entry 5mbr
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
- 5mbr
- Class
- DNA
- Method
- NMR
- Summary
- Quadruplex with flipped tetrad formed by a human telomeric sequence
- Reference
- Dickerhoff J, Haase L, Langel W, Weisz K (2017): "Tracing Effects of Fluorine Substitutions on G-Quadruplex Conformational Changes." ACS Chem. Biol., 12, 1308-1315. doi: 10.1021/acschembio.6b01096.
- Abstract
- A human telomere sequence that folds into an intramolecular (3 + 1)-hybrid G-quadruplex was modified by the incorporation of 2'-fluoro-2'-deoxyriboguanosines ((F)G) into syn positions of its outer tetrad. A circular dichroism and NMR spectral analysis reveals a nearly quantitative switch of the G-tetrad polarity with concerted syn↔anti transitions of all four G residues. These observations follow findings on a (F)G-substituted (3 + 1)-hybrid quadruplex with a different fold, suggesting a more general propensity of hybrid-type quadruplexes to undergo a tetrad polarity reversal. Two out of the three (F)G analogs in both modified quadruplexes adopt an S-type sugar pucker, challenging a sole contribution of N-type sugars in enforcing an anti glycosidic torsion angle associated with the tetrad flip. NMR restrained three-dimensional structures of the two substituted quadruplexes reveal a largely conserved overall fold but significant rearrangements of the overhang and loop nucleotides capping the flipped tetrad. Sugar pucker preferences of the (F)G analogs may be rationalized by different orientations of the fluorine atom and its resistance to be positioned within the narrow groove with its highly negative electrostatic potential and spine of water molecules.
- G4 notes
- 3 G-tetrads, 1 G4 helix, 1 G4 stem, 3(-P-Lw-Ln), hybrid-1(3+1), UUDU
Base-block schematics in six views
List of 3 G-tetrads
1 glyco-bond=--s- sugar=---3 groove=-wn- planarity=0.424 type=other nts=4 ggGg A.GF2/3,A.GF2/9,A.DG17,A.GF2/21 2 glyco-bond=--s- sugar=..-- groove=-wn- planarity=0.273 type=other nts=4 GGGG A.DG4,A.DG10,A.DG16,A.DG22 3 glyco-bond=--s- sugar=.--- groove=-wn- planarity=0.179 type=other nts=4 GGGG A.DG5,A.DG11,A.DG15,A.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-tetrad layers, INTRA-molecular, with 1 stem
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1 glyco-bond=--s- sugar=---3 groove=-wn- WC-->Major nts=4 ggGg A.GF2/3,A.GF2/9,A.DG17,A.GF2/21 2 glyco-bond=--s- sugar=..-- groove=-wn- WC-->Major nts=4 GGGG A.DG4,A.DG10,A.DG16,A.DG22 3 glyco-bond=--s- sugar=.--- groove=-wn- WC-->Major nts=4 GGGG A.DG5,A.DG11,A.DG15,A.DG23 step#1 pm(>>,forward) area=16.09 rise=3.51 twist=23.6 step#2 pm(>>,forward) area=11.60 rise=3.48 twist=29.0 strand#1 DNA glyco-bond=--- sugar=-.. nts=3 gGG A.GF2/3,A.DG4,A.DG5 strand#2 DNA glyco-bond=--- sugar=-.- nts=3 gGG A.GF2/9,A.DG10,A.DG11 strand#3 DNA glyco-bond=sss sugar=--- nts=3 GGG A.DG17,A.DG16,A.DG15 strand#4 DNA glyco-bond=--- sugar=3-- nts=3 gGG A.GF2/21,A.DG22,A.DG23 |
| 2 stacking diagrams | |
 |
1 glyco-bond=--s- sugar=---3 groove=-wn- WC-->Major nts=4 ggGg A.GF2/3,A.GF2/9,A.DG17,A.GF2/21 |
 |
2 glyco-bond=--s- sugar=..-- groove=-wn- WC-->Major nts=4 GGGG A.DG4,A.DG10,A.DG16,A.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-tetrad layers, 3 loops, INTRA-molecular, UUDU, hybrid-(mixed), 3(-P-Lw-Ln), hybrid-1(3+1)
 |
1 glyco-bond=--s- sugar=---3 groove=-wn- WC-->Major nts=4 ggGg A.GF2/3,A.GF2/9,A.DG17,A.GF2/21 2 glyco-bond=--s- sugar=..-- groove=-wn- WC-->Major nts=4 GGGG A.DG4,A.DG10,A.DG16,A.DG22 3 glyco-bond=--s- sugar=.--- groove=-wn- WC-->Major nts=4 GGGG A.DG5,A.DG11,A.DG15,A.DG23 step#1 pm(>>,forward) area=16.09 rise=3.51 twist=23.6 step#2 pm(>>,forward) area=11.60 rise=3.48 twist=29.0 strand#1 U DNA glyco-bond=--- sugar=-.. nts=3 gGG A.GF2/3,A.DG4,A.DG5 strand#2 U DNA glyco-bond=--- sugar=-.- nts=3 gGG A.GF2/9,A.DG10,A.DG11 strand#3 D DNA glyco-bond=sss sugar=--- nts=3 GGG A.DG17,A.DG16,A.DG15 strand#4 U DNA glyco-bond=--- sugar=3-- nts=3 gGG A.GF2/21,A.DG22,A.DG23 loop#1 type=propeller strands=[#1,#2] nts=3 TTA A.DT6,A.DT7,A.DA8 loop#2 type=lateral strands=[#2,#3] nts=3 TTA A.DT12,A.DT13,A.DA14 loop#3 type=lateral strands=[#3,#4] nts=3 TTA A.DT18,A.DT19,A.DA20 |