Summary information

PDB id
8psc
Class
DNA
Method
NMR
Summary
Three-layered basket-type g-quadruplex from a g-rich sequence with five g-runs
Reference
Vianney YM, Schroder N, Jana J, Chojetzki G, Weisz K (2023): "Showcasing Different G-Quadruplex Folds of a G-Rich Sequence: Between Rule-Based Prediction and Butterfly Effect." J.Am.Chem.Soc., 145, 22194-22205. doi: 10.1021/jacs.3c08336.
Abstract
In better understanding the interactions of G-quadruplexes in a cellular or noncellular environment, a reliable sequence-based prediction of their three-dimensional fold would be extremely useful, yet is often limited by their remarkable structural diversity. A G-rich sequence related to a promoter sequence of the PDGFR-β nuclease hypersensitivity element (NHE) comprises a G3-G3-G2-G4-G3 pattern of five G-runs with two to four G residues. Although the predominant formation of three-layered canonical G-quadruplexes with uninterrupted G-columns can be expected, minimal base substitutions in a non-G-tract domain were shown to guide folding into either a basket-type antiparallel quadruplex, a parallel-stranded quadruplex with an interrupted G-column, a quadruplex with a V-shaped loop, or a (3+1) hybrid quadruplex. A 3D NMR structure for each of the different folds was determined. Supported by thermodynamic profiling on additional sequence variants, formed topologies were rationalized by the identification and assessment of specific critical interactions of loop and overhang residues, giving valuable insights into their contribution to favor a particular conformer. The variability of such tertiary interactions, together with only small differences in quadruplex free energies, emphasizes current limits for a reliable sequence-dependent prediction of favored topologies from sequences with multiple irregularly positioned G-tracts.
G4 notes
3 G-tetrads, 1 G4 helix, 1 G4 stem, 3(-LwD+Ln), basket(2+2), UDDU

Base-block schematics in six views

PyMOL session file PDB file View in 3Dmol.js

List of 3 G-tetrads

 1 glyco-bond=s--s sugar=---- groove=w-n- planarity=0.174 type=other  nts=4 GGGG A.DG2,A.DG9,A.DG22,A.DG15
 2 glyco-bond=s--s sugar=---- groove=w-n- planarity=0.176 type=other  nts=4 gGGG A.BGM3,A.DG8,A.DG21,A.DG16
 3 glyco-bond=-ss- sugar=---- groove=w-n- planarity=0.338 type=bowl   nts=4 GGGG A.DG4,A.DG7,A.DG20,A.DG17

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=s--s sugar=---- groove=w-n- Major-->WC nts=4 GGGG A.DG2,A.DG9,A.DG22,A.DG15
 2  glyco-bond=s--s sugar=---- groove=w-n- Major-->WC nts=4 gGGG A.BGM3,A.DG8,A.DG21,A.DG16
 3  glyco-bond=-ss- sugar=---- groove=w-n- WC-->Major nts=4 GGGG A.DG4,A.DG7,A.DG20,A.DG17
  step#1  mp(<<,backward) area=13.13 rise=3.46 twist=26.3
  step#2  mm(<>,outward)  area=18.17 rise=3.55 twist=14.9
  strand#1 DNA glyco-bond=ss- sugar=--- nts=3 GgG A.DG2,A.BGM3,A.DG4
  strand#2 DNA glyco-bond=--s sugar=--- nts=3 GGG A.DG9,A.DG8,A.DG7
  strand#3 DNA glyco-bond=--s sugar=--- nts=3 GGG A.DG22,A.DG21,A.DG20
  strand#4 DNA glyco-bond=ss- sugar=--- nts=3 GGG A.DG15,A.DG16,A.DG17

Download PDB file
Interactive view in 3Dmol.js

2 stacking diagrams
 1  glyco-bond=s--s sugar=---- groove=w-n- Major-->WC nts=4 GGGG A.DG2,A.DG9,A.DG22,A.DG15
2 glyco-bond=s--s sugar=---- groove=w-n- Major-->WC nts=4 gGGG A.BGM3,A.DG8,A.DG21,A.DG16
step#1 mp(<<,backward) area=13.13 rise=3.46 twist=26.3

Download PDB file
Interactive view in 3Dmol.js

 2  glyco-bond=s--s sugar=---- groove=w-n- Major-->WC nts=4 gGGG A.BGM3,A.DG8,A.DG21,A.DG16
3 glyco-bond=-ss- sugar=---- groove=w-n- WC-->Major nts=4 GGGG A.DG4,A.DG7,A.DG20,A.DG17
step#2 mm(<>,outward) area=18.17 rise=3.55 twist=14.9

Download PDB file
Interactive view in 3Dmol.js

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, UDDU, anti-parallel, 3(-LwD+Ln), basket(2+2)

 1  glyco-bond=s--s sugar=---- groove=w-n- Major-->WC nts=4 GGGG A.DG2,A.DG9,A.DG22,A.DG15
 2  glyco-bond=s--s sugar=---- groove=w-n- Major-->WC nts=4 gGGG A.BGM3,A.DG8,A.DG21,A.DG16
 3  glyco-bond=-ss- sugar=---- groove=w-n- WC-->Major nts=4 GGGG A.DG4,A.DG7,A.DG20,A.DG17
  step#1  mp(<<,backward) area=13.13 rise=3.46 twist=26.3
  step#2  mm(<>,outward)  area=18.17 rise=3.55 twist=14.9
  strand#1  U DNA glyco-bond=ss- sugar=--- nts=3 GgG A.DG2,A.BGM3,A.DG4
  strand#2  D DNA glyco-bond=--s sugar=--- nts=3 GGG A.DG9,A.DG8,A.DG7
  strand#3  D DNA glyco-bond=--s sugar=--- nts=3 GGG A.DG22,A.DG21,A.DG20
  strand#4  U DNA glyco-bond=ss- sugar=--- nts=3 GGG A.DG15,A.DG16,A.DG17
  loop#1 type=lateral   strands=[#1,#2] nts=2 TA A.DT5,A.DA6
  loop#2 type=diagonal  strands=[#2,#4] nts=5 CGGCG A.DC10,A.DG11,A.DG12,A.DC13,A.DG14
  loop#3 type=lateral   strands=[#4,#3] nts=2 CA A.DC18,A.DA19

Download PDB file
Interactive view in 3Dmol.js