Summary information and primary citation

PDB-id
6fq2
Class
DNA
Method
X-ray (2.31 Å)
Summary
Structure of minimal sequence for left -handed g-quadruplex formation
Reference
Bakalar B, Heddi B, Schmitt E, Mechulam Y, Phan AT (2019): "A Minimal Sequence for Left-Handed G-Quadruplex Formation." Angew. Chem. Int. Ed. Engl., 58, 2331-2335. doi: 10.1002/anie.201812628.
Abstract
Recently, we observed the first example of a left-handed G-quadruplex structure formed by natural DNA, named Z-G4. We analysed the Z-G4 structure and inspected its primary 28-nt sequence in order to identify motifs that convey the unique left-handed twist. Using circular dichroism spectroscopy, NMR spectroscopy, and X-ray crystallography, we revealed a minimal sequence motif of 12 nt (GTGGTGGTGGTG) for formation of the left-handed DNA G-quadruplex, which is found to be highly abundant in the human genome. A systematic analysis of thymine loop mutations revealed a moderate sequence tolerance, which would further broaden the space of sequences prone to left-handed G-quadruplex formation.
G4 notes
4 G-tetrads, 1 G4 helix

Cartoon-block schematics in six views (download the tarball)

PyMOL session file

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List of 4 G-tetrads

 1 glyco-bond=---- sugar=---- groove=---- planarity=0.119 type=planar O+ nts=4 GGGG A.DG1,A.DG4,A.DG7,A.DG10
 2 glyco-bond=---- sugar=---- groove=---- planarity=0.312 type=other  O+ nts=4 GGGG A.DG3,A.DG6,A.DG9,A.DG12
 3 glyco-bond=---- sugar=---- groove=---- planarity=0.114 type=planar O+ nts=4 GGGG B.DG1,B.DG4,B.DG7,B.DG10
 4 glyco-bond=---- sugar=---- groove=---- planarity=0.327 type=other  O+ nts=4 GGGG B.DG3,B.DG6,B.DG9,B.DG12

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, 4 G-tetrads, inter-molecular
 1  glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG A.DG3,A.DG6,A.DG9,A.DG12
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG A.DG4,A.DG7,A.DG10,A.DG1
 3  glyco-bond=---- sugar=---- groove=---- Major-->WC O+ nts=4 GGGG B.DG7,B.DG4,B.DG1,B.DG10
 4  glyco-bond=---- sugar=---- groove=---- Major-->WC O+ nts=4 GGGG B.DG6,B.DG3,B.DG12,B.DG9
  step#1  mp(<<,backward) area=11.25 rise=3.38 twist=-25.8
  step#2  mm(<>,outward)  area=29.76 rise=3.26 twist=-11.8
  step#3  pm(>>,forward)  area=10.59 rise=3.30 twist=-25.9
  strand#1 DNA glyco-bond=---- sugar=---- nts=4 GGGG A.DG3,A.DG4,B.DG7,B.DG6
  strand#2 DNA glyco-bond=---- sugar=---- nts=4 GGGG A.DG6,A.DG7,B.DG4,B.DG3
  strand#3 DNA glyco-bond=---- sugar=---- nts=4 GGGG A.DG9,A.DG10,B.DG1,B.DG12
  strand#4 DNA glyco-bond=---- sugar=---- nts=4 GGGG A.DG12,A.DG1,B.DG10,B.DG9

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3 stacking diagrams 
 1  glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG A.DG3,A.DG6,A.DG9,A.DG12
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG A.DG4,A.DG7,A.DG10,A.DG1
  step#1  mp(<<,backward) area=11.25 rise=3.38 twist=-25.8

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Interactive view in 3Dmol.js

 
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG A.DG4,A.DG7,A.DG10,A.DG1
 3  glyco-bond=---- sugar=---- groove=---- Major-->WC O+ nts=4 GGGG B.DG7,B.DG4,B.DG1,B.DG10
  step#2  mm(<>,outward)  area=29.76 rise=3.26 twist=-11.8

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Interactive view in 3Dmol.js

 
 3  glyco-bond=---- sugar=---- groove=---- Major-->WC O+ nts=4 GGGG B.DG7,B.DG4,B.DG1,B.DG10
 4  glyco-bond=---- sugar=---- groove=---- Major-->WC O+ nts=4 GGGG B.DG6,B.DG3,B.DG12,B.DG9
  step#3  pm(>>,forward)  area=10.59 rise=3.30 twist=-25.9

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Interactive view in 3Dmol.js

List of 4 non-stem G4-loops (including the two closing Gs)

 1 type=V-shaped  helix=#1 nts=4 GTGG A.DG1,A.DT2,A.DG3,A.DG4
 2* type=V-shaped  helix=#1 nts=4 GGTG A.DG9,A.DG10,A.DT11,A.DG12
 3 type=V-shaped  helix=#1 nts=4 GTGG B.DG1,B.DT2,B.DG3,B.DG4
 4* type=V-shaped  helix=#1 nts=4 GGTG B.DG9,B.DG10,B.DT11,B.DG12