Summary information

PDB id
6jce
Class
DNA
Method
NMR
Summary
NMR solution and x-ray crystal structures of a DNA containing both right-and left-handed parallel-stranded g-quadruplexes
Reference
Winnerdy FR, Bakalar B, Maity A, Vandana JJ, Mechulam Y, Schmitt E, Phan AT (2019): "NMR solution and X-ray crystal structures of a DNA molecule containing both right- and left-handed parallel-stranded G-quadruplexes." Nucleic Acids Res., 47, 8272-8281. doi: 10.1093/nar/gkz349.
Abstract
Analogous to the B- and Z-DNA structures in double-helix DNA, there exist both right- and left-handed quadruple-helix (G-quadruplex) DNA. Numerous conformations of right-handed and a few left-handed G-quadruplexes were previously observed, yet they were always identified separately. Here, we present the NMR solution and X-ray crystal structures of a right- and left-handed hybrid G-quadruplex. The structure reveals a stacking interaction between two G-quadruplex blocks with different helical orientations and displays features of both right- and left-handed G-quadruplexes. An analysis of loop mutations suggests that single-nucleotide loops are preferred or even required for the left-handed G-quadruplex formation. The discovery of a right- and left-handed hybrid G-quadruplex further expands the polymorphism of G-quadruplexes and is potentially useful in designing a left-to-right junction in G-quadruplex engineering.
G4 notes
4 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 4 G-tetrads

 1 glyco-bond=---- sugar=---- groove=---- planarity=0.049 type=planar nts=4 GGGG A.DG1,A.DG5,A.DG10,A.DG14
 2 glyco-bond=---- sugar=---- groove=---- planarity=0.113 type=planar nts=4 GGGG A.DG2,A.DG6,A.DG11,A.DG15
 3 glyco-bond=---- sugar=---- groove=---- planarity=0.162 type=other  nts=4 GGGG A.DG18,A.DG21,A.DG24,A.DG27
 4 glyco-bond=---- sugar=---- groove=---- planarity=0.307 type=other  nts=4 GGGG A.DG20,A.DG23,A.DG26,A.DG29

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-tetrad layers, INTRA-molecular, with 1 stem

 1  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG2,A.DG6,A.DG11,A.DG15
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG1,A.DG5,A.DG10,A.DG14
 3  glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG A.DG27,A.DG24,A.DG21,A.DG18
 4  glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG A.DG26,A.DG23,A.DG20,A.DG29
  step#1  mp(<<,backward) area=10.89 rise=3.06 twist=32.4
  step#2  mm(<>,outward)  area=31.50 rise=3.75 twist=-19.2
  step#3  pm(>>,forward)  area=9.38  rise=2.87 twist=-30.0
  strand#1 DNA glyco-bond=---- sugar=---- nts=4 GGGG A.DG2,A.DG1,A.DG27,A.DG26
  strand#2 DNA glyco-bond=---- sugar=---- nts=4 GGGG A.DG6,A.DG5,A.DG24,A.DG23
  strand#3 DNA glyco-bond=---- sugar=---- nts=4 GGGG A.DG11,A.DG10,A.DG21,A.DG20
  strand#4 DNA glyco-bond=---- sugar=---- nts=4 GGGG A.DG15,A.DG14,A.DG18,A.DG29

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3 stacking diagrams 
 1  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG2,A.DG6,A.DG11,A.DG15
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG1,A.DG5,A.DG10,A.DG14
  step#1  mp(<<,backward) area=10.89 rise=3.06 twist=32.4

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 2  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG1,A.DG5,A.DG10,A.DG14
 3  glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG A.DG27,A.DG24,A.DG21,A.DG18
  step#2  mm(<>,outward)  area=31.50 rise=3.75 twist=-19.2

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 3  glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG A.DG27,A.DG24,A.DG21,A.DG18
 4  glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG A.DG26,A.DG23,A.DG20,A.DG29
  step#3  pm(>>,forward)  area=9.38  rise=2.87 twist=-30.0

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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.DG1,A.DG5,A.DG10,A.DG14
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG2,A.DG6,A.DG11,A.DG15
  step#1  pm(>>,forward)  area=10.89 rise=3.06 twist=32.4
  strand#1  U DNA glyco-bond=-- sugar=-- nts=2 GG A.DG1,A.DG2
  strand#2  U DNA glyco-bond=-- sugar=-- nts=2 GG A.DG5,A.DG6
  strand#3  U DNA glyco-bond=-- sugar=-- nts=2 GG A.DG10,A.DG11
  strand#4  U DNA glyco-bond=-- sugar=-- nts=2 GG A.DG14,A.DG15
  loop#1 type=propeller strands=[#1,#2] nts=2 TT A.DT3,A.DT4
  loop#2 type=propeller strands=[#2,#3] nts=3 TGT A.DT7,A.DG8,A.DT9
  loop#3 type=propeller strands=[#3,#4] nts=2 TT A.DT12,A.DT13

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List of 2 non-stem G4-loops (including the two closing Gs)

 1 type=V-shaped  helix=#1 nts=4 GTGG A.DG18,A.DT19,A.DG20,A.DG21
 2* type=V-shaped  helix=#1 nts=4 GGTG A.DG26,A.DG27,A.DT28,A.DG29