Summary information

PDB id
6zte
Class
DNA
Method
NMR
Summary
Structure of a parallel c-myc modified with 5' duplex stem-loop and 3' diagonal snap-back loop
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 side chain was shown to bind the Q-D hybrids with a very high affinity in the order Ka ≈107  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, 2(-P-P-P), parallel(4+0), UUUU

Base-block schematics in six views

PyMOL session file PDB file View in 3Dmol.js

List of 3 G-tetrads

 1 glyco-bond=---- sugar=---- groove=---- planarity=0.327 type=other  nts=4 GGGG A.DG18,A.DG22,A.DG25,A.DG29
 2 glyco-bond=---- sugar=---- groove=---- planarity=0.426 type=other  nts=4 GGGG A.DG19,A.DG23,A.DG26,A.DG30
 3 glyco-bond=-s-- sugar=-.-- groove=wn-- planarity=0.381 type=saddle nts=4 GGGG A.DG20,A.DG36,A.DG27,A.DG31

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.DG18,A.DG22,A.DG25,A.DG29
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG19,A.DG23,A.DG26,A.DG30
 3  glyco-bond=-s-- sugar=-.-- groove=wn-- WC-->Major nts=4 GGGG A.DG20,A.DG36,A.DG27,A.DG31
  step#1  pm(>>,forward)  area=11.09 rise=3.42 twist=30.5
  step#2  pm(>>,forward)  area=15.38 rise=3.47 twist=24.8
  strand#1 DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG18,A.DG19,A.DG20
  strand#2 DNA glyco-bond=--s sugar=--. nts=3 GGG A.DG22,A.DG23,A.DG36
  strand#3 DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG25,A.DG26,A.DG27
  strand#4 DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG29,A.DG30,A.DG31

Download PDB file
Interactive view in 3Dmol.js
2 stacking diagrams 
 1  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG18,A.DG22,A.DG25,A.DG29
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG19,A.DG23,A.DG26,A.DG30
  step#1  pm(>>,forward)  area=11.09 rise=3.42 twist=30.5

Download PDB file
Interactive view in 3Dmol.js

 
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG19,A.DG23,A.DG26,A.DG30
 3  glyco-bond=-s-- sugar=-.-- groove=wn-- WC-->Major nts=4 GGGG A.DG20,A.DG36,A.DG27,A.DG31
  step#2  pm(>>,forward)  area=15.38 rise=3.47 twist=24.8

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, 2 G-tetrad layers, 3 loops, INTRA-molecular, UUUU, parallel, 2(-P-P-P), parallel(4+0)

 1  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG18,A.DG22,A.DG25,A.DG29
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG19,A.DG23,A.DG26,A.DG30
  step#1  pm(>>,forward)  area=11.09 rise=3.42 twist=30.5
  strand#1  U DNA glyco-bond=-- sugar=-- nts=2 GG A.DG18,A.DG19
  strand#2  U DNA glyco-bond=-- sugar=-- nts=2 GG A.DG22,A.DG23
  strand#3  U DNA glyco-bond=-- sugar=-- nts=2 GG A.DG25,A.DG26
  strand#4  U DNA glyco-bond=-- sugar=-- nts=2 GG A.DG29,A.DG30
  loop#1 type=propeller strands=[#1,#2] nts=2 GT A.DG20,A.DT21
  loop#2 type=propeller strands=[#2,#3] nts=1 T A.DT24
  loop#3 type=propeller strands=[#3,#4] nts=2 GT A.DG27,A.DT28

Download PDB file
Interactive view in 3Dmol.js

List of 1 non-stem G4-loop (including the two closing Gs)

 1 type=diagonal  helix=#1 nts=6 GGAAGG A.DG31,A.DG32,A.DA33,A.DA34,A.DG35,A.DG36