Summary information

PDB id
5ov2
Class
DNA
Method
NMR
Summary
2'f-ana-g modified quadruplex with a flipped tetrad
Reference
Dickerhoff J, Weisz K (2017): "Nonconventional C-HF Hydrogen Bonds Support a Tetrad Flip in Modified G-Quadruplexes." J Phys Chem Lett, 8, 5148-5152. doi: 10.1021/acs.jpclett.7b02428.
Abstract
A G-quadruplex adopting a (3 + 1)-hybrid structure was substituted at its 5'-tetrad by 2'-deoxy-2'-fluoro-arabinoguanosine ((F)araG) analogs. Incorporation of anti-favoring (F)araG at syn-positions of the 5'-outer tetrad induced a reversal of the tetrad polarity without noticeably compromising the quadruplex stability. This conformational change is shown to be promoted by nonconventional C-H···F hydrogen bonds acting within the anti-(F)araG residues.
G4 notes
3 G-tetrads, 1 G4 helix, 1 G4 stem, 3(-PD+Lw), U3D(3+1), UUUD

Base-block schematics in six views

PyMOL session file PDB file View in 3Dmol.js

List of 3 G-tetrads

 1 glyco-bond=---s sugar=---- groove=--wn planarity=0.372 type=other  nts=4 gggG X.GFL1,X.GFL6,X.GFL20,X.DG16
 2 glyco-bond=---s sugar=---- groove=--wn planarity=0.393 type=other  nts=4 GGGG X.DG2,X.DG7,X.DG21,X.DG15
 3 glyco-bond=---s sugar=.--- groove=--wn planarity=0.279 type=saddle nts=4 GGGG X.DG3,X.DG8,X.DG22,X.DG14

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=---s sugar=---- groove=--wn WC-->Major nts=4 gggG X.GFL1,X.GFL6,X.GFL20,X.DG16
 2  glyco-bond=---s sugar=---- groove=--wn WC-->Major nts=4 GGGG X.DG2,X.DG7,X.DG21,X.DG15
 3  glyco-bond=---s sugar=.--- groove=--wn WC-->Major nts=4 GGGG X.DG3,X.DG8,X.DG22,X.DG14
  step#1  pm(>>,forward)  area=15.84 rise=3.46 twist=24.0
  step#2  pm(>>,forward)  area=13.68 rise=3.47 twist=27.3
  strand#1 DNA glyco-bond=--- sugar=--. nts=3 gGG X.GFL1,X.DG2,X.DG3
  strand#2 DNA glyco-bond=--- sugar=--- nts=3 gGG X.GFL6,X.DG7,X.DG8
  strand#3 DNA glyco-bond=--- sugar=--- nts=3 gGG X.GFL20,X.DG21,X.DG22
  strand#4 DNA glyco-bond=sss sugar=--- nts=3 GGG X.DG16,X.DG15,X.DG14

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2 stacking diagrams 
 1  glyco-bond=---s sugar=---- groove=--wn WC-->Major nts=4 gggG X.GFL1,X.GFL6,X.GFL20,X.DG16
 2  glyco-bond=---s sugar=---- groove=--wn WC-->Major nts=4 GGGG X.DG2,X.DG7,X.DG21,X.DG15
  step#1  pm(>>,forward)  area=15.84 rise=3.46 twist=24.0

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 2  glyco-bond=---s sugar=---- groove=--wn WC-->Major nts=4 GGGG X.DG2,X.DG7,X.DG21,X.DG15
 3  glyco-bond=---s sugar=.--- groove=--wn WC-->Major nts=4 GGGG X.DG3,X.DG8,X.DG22,X.DG14
  step#2  pm(>>,forward)  area=13.68 rise=3.47 twist=27.3

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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, 3 loops, INTRA-molecular, UUUD, hybrid-(mixed), 3(-PD+Lw), U3D(3+1)

 1  glyco-bond=---s sugar=---- groove=--wn WC-->Major nts=4 gggG X.GFL1,X.GFL6,X.GFL20,X.DG16
 2  glyco-bond=---s sugar=---- groove=--wn WC-->Major nts=4 GGGG X.DG2,X.DG7,X.DG21,X.DG15
 3  glyco-bond=---s sugar=.--- groove=--wn WC-->Major nts=4 GGGG X.DG3,X.DG8,X.DG22,X.DG14
  step#1  pm(>>,forward)  area=15.84 rise=3.46 twist=24.0
  step#2  pm(>>,forward)  area=13.68 rise=3.47 twist=27.3
  strand#1  U DNA glyco-bond=--- sugar=--. nts=3 gGG X.GFL1,X.DG2,X.DG3
  strand#2  U DNA glyco-bond=--- sugar=--- nts=3 gGG X.GFL6,X.DG7,X.DG8
  strand#3  U DNA glyco-bond=--- sugar=--- nts=3 gGG X.GFL20,X.DG21,X.DG22
  strand#4  D DNA glyco-bond=sss sugar=--- nts=3 GGG X.DG16,X.DG15,X.DG14
  loop#1 type=propeller strands=[#1,#2] nts=2 AT X.DA4,X.DT5
  loop#2 type=diagonal  strands=[#2,#4] nts=5 ACACA X.DA9,X.DC10,X.DA11,X.DC12,X.DA13
  loop#3 type=lateral   strands=[#4,#3] nts=3 GAC X.DG17,X.DA18,X.DC19

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