Summary information

PDB id
2n60
Class
DNA
Method
NMR
Summary
G-quadruplexes with (4n-1) guanines in the g-tetrad core: formation of a g-triad water complex and implication for small-molecule binding
Reference
Heddi B, Martin-Pintado N, Serimbetov Z, Kari TM, Phan AT (2016): "G-quadruplexes with (4n - 1) guanines in the G-tetrad core: formation of a G-triadwater complex and implication for small-molecule binding." Nucleic Acids Res., 44, 910-916. doi: 10.1093/nar/gkv1357.
Abstract
G-quadruplexes are non-canonical structures of nucleic acids, in which guanine bases form planar G-tetrads (G·G·G·G) that stack on each other in the core of the structure. G-quadruplexes generally contain multiple times of four (4n) guanines in the core. Here, we study the structure of G-quadruplexes with only (4n - 1) guanines in the core. The solution structure of a DNA sequence containing 11 guanines showed the formation of a parallel G-quadruplex involving two G-tetrads and one G-triad with a vacant site. Molecular dynamics simulation established the formation of a stable G-triad·water complex, where water molecules mimic the position of the missing guanine in the vacant site. The concept of forming G-quadruplexes with missing guanines in the core broadens the current definition of G-quadruplex-forming sequences. The potential ability of such structures to bind different metabolites, including guanine, guanosine and GTP, in the vacant site, could have biological implications in regulatory functions. Formation of this unique binding pocket in the G-triad could be used as a specific target in drug design.
G4 notes
2 G-tetrads, 1 G4 helix, 1 G4 stem, 2(-P-P-P), parallel(4+0), UUUU

Base-block schematics in six views

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List of 2 G-tetrads

 1 glyco-bond=---- sugar=.--- groove=---- planarity=0.362 type=other  nts=4 GGGG A.DG3,A.DG7,A.DG11,A.DG15
 2 glyco-bond=---- sugar=---- groove=---- planarity=0.362 type=other  nts=4 GGGG A.DG5,A.DG8,A.DG12,A.DG16

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, 2 G-tetrad layers, INTRA-molecular, with 1 stem

 1  glyco-bond=---- sugar=.--- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG7,A.DG11,A.DG15
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG5,A.DG8,A.DG12,A.DG16
  step#1  pm(>>,forward)  area=13.88 rise=3.43 twist=30.7
  strand#1 DNA glyco-bond=-- sugar=.- nts=2 GG A.DG3,A.DG5
  strand#2 DNA glyco-bond=-- sugar=-- nts=2 GG A.DG7,A.DG8
  strand#3 DNA glyco-bond=-- sugar=-- nts=2 GG A.DG11,A.DG12
  strand#4 DNA glyco-bond=-- sugar=-- nts=2 GG A.DG15,A.DG16

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1 stacking diagram 
 1  glyco-bond=---- sugar=.--- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG7,A.DG11,A.DG15
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG5,A.DG8,A.DG12,A.DG16
  step#1  pm(>>,forward)  area=13.88 rise=3.43 twist=30.7

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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.DG3,A.DG7,A.DG11,A.DG15
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG5,A.DG8,A.DG12,A.DG16
  step#1  pm(>>,forward)  area=13.88 rise=3.43 twist=30.7
  strand#1* U DNA glyco-bond=-- sugar=.- nts=2 GG A.DG3,A.DG5 bulged-nts=1 T A.DT4
  strand#2  U DNA glyco-bond=-- sugar=-- nts=2 GG A.DG7,A.DG8
  strand#3  U DNA glyco-bond=-- sugar=-- nts=2 GG A.DG11,A.DG12
  strand#4  U DNA glyco-bond=-- sugar=-- nts=2 GG A.DG15,A.DG16
  loop#1 type=propeller strands=[#1,#2] nts=1 T A.DT6
  loop#2 type=propeller strands=[#2,#3] nts=2 GT A.DG9,A.DT10
  loop#3 type=propeller strands=[#3,#4] nts=2 GT A.DG13,A.DT14

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