Summary information

PDB id
7v6v
Class
DNA
Method
NMR
Summary
Trimolecular g-quadruplexes consists of a hairpin motif and two short chains
Reference
Hu W, Jing H, Fu W, Wang Z, Zhou J, Zhang N (2023): "Conversion to Trimolecular G-Quadruplex by Spontaneous Hoogsteen Pairing-Based Strand Displacement Reaction between Bimolecular G-Quadruplex and Double G-Rich Probes." J.Am.Chem.Soc. doi: 10.1021/jacs.3c05617.
Abstract
Bimolecular or tetramolecular G-quadruplexes (GQs) are predominantly self-assembled by the same sequence-identical G-rich oligonucleotides and usually remain inert to the strand displacement reaction (SDR) with other short G-rich invading fragments of DNA or RNA. Appealingly, in this study, we demonstrate that a parallel homomeric bimolecular GQ target of
G4 notes
3 G-tetrads, 1 G4 helix, 1 G4 stem, parallel(4+0), UUUU

Base-block schematics in six views

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List of 3 G-tetrads

 1 glyco-bond=---- sugar=---- groove=---- planarity=0.337 type=bowl   nts=4 GGGG A.DG3,A.DG7,B.DG12,C.DG17
 2 glyco-bond=---- sugar=---- groove=---- planarity=0.322 type=bowl   nts=4 GGGG A.DG4,A.DG8,B.DG13,C.DG18
 3 glyco-bond=---- sugar=---- groove=---- planarity=0.393 type=bowl   nts=4 GGGG A.DG5,A.DG9,B.DG14,C.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, inter-molecular, with 1 stem

 1  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG7,B.DG12,C.DG17
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG8,B.DG13,C.DG18
 3  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG5,A.DG9,B.DG14,C.DG19
  step#1  pm(>>,forward)  area=13.51 rise=3.44 twist=28.6
  step#2  pm(>>,forward)  area=13.28 rise=3.75 twist=28.3
  strand#1 DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG3,A.DG4,A.DG5
  strand#2 DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG7,A.DG8,A.DG9
  strand#3 DNA glyco-bond=--- sugar=--- nts=3 GGG B.DG12,B.DG13,B.DG14
  strand#4 DNA glyco-bond=--- sugar=--- nts=3 GGG C.DG17,C.DG18,C.DG19

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2 stacking diagrams 
 1  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG7,B.DG12,C.DG17
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG8,B.DG13,C.DG18
  step#1  pm(>>,forward)  area=13.51 rise=3.44 twist=28.6

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 2  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG8,B.DG13,C.DG18
 3  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG5,A.DG9,B.DG14,C.DG19
  step#2  pm(>>,forward)  area=13.28 rise=3.75 twist=28.3

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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, 3 G-tetrad layers, 1 loops, inter-molecular, UUUU, parallel, parallel(4+0)

 1  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG7,B.DG12,C.DG17
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG8,B.DG13,C.DG18
 3  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG5,A.DG9,B.DG14,C.DG19
  step#1  pm(>>,forward)  area=13.51 rise=3.44 twist=28.6
  step#2  pm(>>,forward)  area=13.28 rise=3.75 twist=28.3
  strand#1  U DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG3,A.DG4,A.DG5
  strand#2  U DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG7,A.DG8,A.DG9
  strand#3  U DNA glyco-bond=--- sugar=--- nts=3 GGG B.DG12,B.DG13,B.DG14
  strand#4  U DNA glyco-bond=--- sugar=--- nts=3 GGG C.DG17,C.DG18,C.DG19
  loop#1 type=propeller strands=[#1,#2] nts=1 A A.DA6

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