Detailed DSSR results for the G-quadruplex: PDB entry 6zl2
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
- 6zl2
- Class
- DNA
- Method
- NMR
- Summary
- Structure of a parallel c-myc modified with 3' duplex stem-loop overhang
- Reference
- Vianney YM, Preckwinkel P, Mohr S, Weisz K (2020): "Quadruplex-Duplex Junction: A High-Affinity Binding Site for Indoloquinoline Ligands." Chemistry, 26, 16910-16922. doi: 10.1002/chem.202003540.
- Abstract
- A parallel quadruplex derived from the Myc promoter sequence was extended by a stem-loop duplex at either its 5'- or 3'-terminus to mimic a quadruplex-duplex (Q-D) junction as a potential genomic target. High-resolution structures of the hybrids demonstrate continuous stacking of the duplex on the quadruplex core without significant perturbations. An indoloquinoline ligand carrying an aminoalkyl sidechain was shown to bind the Q-D hybrids with a very high affinity in the order K a ~ 10 7 M -1 irrespective of the duplex location at the quadruplex 3'- or 5'-end. NMR chemical shift perturbations identified the tetrad face of the Q-D junction as specific binding site for the ligand. However, calorimetric analyses revealed significant differences in the thermodynamic profiles upon binding to hybrids with either a duplex extension at the quadruplex 3'- or 5'-terminus. A large enthalpic gain and considerable hydrophobic effects are accompanied by the binding of one ligand to the 3'-Q-D junction, whereas non-hydrophobic entropic contributions favor binding with formation of a 2:1 ligand-quadruplex complex in case of the 5'-Q-D hybrid.
- 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=0.370 type=other nts=4 GGGG A.DG4,A.DG8,A.DG13,A.DG17 2 glyco-bond=---- sugar=-... groove=---- planarity=0.283 type=other nts=4 GGGG A.DG5,A.DG9,A.DG14,A.DG18 3 glyco-bond=---- sugar=---- groove=---- planarity=0.179 type=other nts=4 GGGG A.DG6,A.DG10,A.DG15,A.DG19
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.DG4,A.DG8,A.DG13,A.DG17 2 glyco-bond=---- sugar=-... groove=---- WC-->Major nts=4 GGGG A.DG5,A.DG9,A.DG14,A.DG18 3 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG6,A.DG10,A.DG15,A.DG19 step#1 pm(>>,forward) area=15.73 rise=3.47 twist=25.9 step#2 pm(>>,forward) area=15.05 rise=3.41 twist=24.7 strand#1 DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG4,A.DG5,A.DG6 strand#2 DNA glyco-bond=--- sugar=-.- nts=3 GGG A.DG8,A.DG9,A.DG10 strand#3 DNA glyco-bond=--- sugar=..- nts=3 GGG A.DG13,A.DG14,A.DG15 strand#4 DNA glyco-bond=--- sugar=-.- nts=3 GGG A.DG17,A.DG18,A.DG19 |
| 2 stacking diagrams | |
 |
1 glyco-bond=---- sugar=--.- groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG8,A.DG13,A.DG17 |
 |
2 glyco-bond=---- sugar=-... groove=---- WC-->Major nts=4 GGGG A.DG5,A.DG9,A.DG14,A.DG18 |
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.DG4,A.DG8,A.DG13,A.DG17 2 glyco-bond=---- sugar=-... groove=---- WC-->Major nts=4 GGGG A.DG5,A.DG9,A.DG14,A.DG18 3 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG6,A.DG10,A.DG15,A.DG19 step#1 pm(>>,forward) area=15.73 rise=3.47 twist=25.9 step#2 pm(>>,forward) area=15.05 rise=3.41 twist=24.7 strand#1 U DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG4,A.DG5,A.DG6 strand#2 U DNA glyco-bond=--- sugar=-.- nts=3 GGG A.DG8,A.DG9,A.DG10 strand#3 U DNA glyco-bond=--- sugar=..- nts=3 GGG A.DG13,A.DG14,A.DG15 strand#4 U DNA glyco-bond=--- sugar=-.- nts=3 GGG A.DG17,A.DG18,A.DG19 loop#1 type=propeller strands=[#1,#2] nts=1 T A.DT7 loop#2 type=propeller strands=[#2,#3] nts=2 TA A.DT11,A.DA12 loop#3 type=propeller strands=[#3,#4] nts=1 T A.DT16 |