Summary information [schematics · tetrads · helices · stems · costacks · homepage]

PDB-id
6f4z
Class
DNA
Method
NMR
Summary
2'f-arag modified quadruplex with flipped g-tract and central tetrad
Reference
Dickerhoff, J., Weisz, K.: (2018) "Fluorine-Mediated Editing of a G-Quadruplex Folding Pathway." Chembiochem, 19, 927-930.
Abstract
A (3+1)-hybrid-type G-quadruplex was substituted within its central tetrad by a single 2'-fluoro-modified guanosine. Driven by the anti-favoring nucleoside analogue, a novel quadruplex fold with inversion of a single G-tract and conversion of a propeller loop into a lateral loop emerges. In addition, scalar couplings across hydrogen bonds demonstrate the formation of intra- and inter-residual F⋅⋅⋅H8-C8 pseudo-hydrogen bonds within the modified quadruplexes. Alternative folding can be rationalized by the impact of fluorine on intermediate species on the basis of a kinetic partitioning mechanism. Apparently, chemical or other environmental perturbations are able to redirect folding of a quadruplex, possibly modulating its regulatory role in physiological processes.
G4 notes
3 G-tetrads, 1 G4 helix, 1 G4 stem · 3(+LnD-Lw), basket(2+2), UUDD

Base-block schematics in six views [summary · tetrads · helices · stems · costacks · homepage]

PyMOL session file PDB file View in 3Dmol.js

List of 3 G-tetrads [summary · schematics · helices · stems · costacks · homepage]

 1 glyco-bond=ss-- groove=-w-n planarity=0.276 type=other  nts=4 GGGG A.DG1,A.DG14,A.DG22,A.DG8
 2 glyco-bond=--ss groove=-w-n planarity=0.202 type=other  nts=4 GgGG A.DG2,A.GFL15,A.DG21,A.DG7
 3 glyco-bond=--ss groove=-w-n planarity=0.265 type=other  nts=4 GGGG A.DG3,A.DG16,A.DG20,A.DG6

List of 1 G4-helix [summary · schematics · tetrads · stems · costacks · homepage]

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=ss-- groove=-w-n Major-->WC nts=4 GGGG A.DG1,A.DG14,A.DG22,A.DG8
 2  glyco-bond=--ss groove=-w-n WC-->Major nts=4 GgGG A.DG2,A.GFL15,A.DG21,A.DG7
 3  glyco-bond=--ss groove=-w-n WC-->Major nts=4 GGGG A.DG3,A.DG16,A.DG20,A.DG6
  step#1  mm(<>,outward)  area=15.75 rise=3.57 twist=14.6
  step#2  pm(>>,forward)  area=11.22 rise=3.44 twist=29.1
  strand#1 DNA glyco-bond=s-- nts=3 GGG A.DG1,A.DG2,A.DG3
  strand#2 DNA glyco-bond=s-- nts=3 GgG A.DG14,A.GFL15,A.DG16
  strand#3 DNA glyco-bond=-ss nts=3 GGG A.DG22,A.DG21,A.DG20
  strand#4 DNA glyco-bond=-ss nts=3 GGG A.DG8,A.DG7,A.DG6

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2 stacking diagrams
 1  glyco-bond=ss-- groove=-w-n Major-->WC nts=4 GGGG A.DG1,A.DG14,A.DG22,A.DG8
2 glyco-bond=--ss groove=-w-n WC-->Major nts=4 GgGG A.DG2,A.GFL15,A.DG21,A.DG7
step#1 mm(<>,outward) area=15.75 rise=3.57 twist=14.6

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 2  glyco-bond=--ss groove=-w-n WC-->Major nts=4 GgGG A.DG2,A.GFL15,A.DG21,A.DG7
3 glyco-bond=--ss groove=-w-n WC-->Major nts=4 GGGG A.DG3,A.DG16,A.DG20,A.DG6
step#2 pm(>>,forward) area=11.22 rise=3.44 twist=29.1

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List of 1 G4-stem [summary · schematics · tetrads · helices · costacks · homepage]

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, UUDD, anti-parallel, 3(+LnD-Lw), basket(2+2)

 1  glyco-bond=ss-- groove=-w-n Major-->WC nts=4 GGGG A.DG1,A.DG14,A.DG22,A.DG8
 2  glyco-bond=--ss groove=-w-n WC-->Major nts=4 GgGG A.DG2,A.GFL15,A.DG21,A.DG7
 3  glyco-bond=--ss groove=-w-n WC-->Major nts=4 GGGG A.DG3,A.DG16,A.DG20,A.DG6
  step#1  mm(<>,outward)  area=15.75 rise=3.57 twist=14.6
  step#2  pm(>>,forward)  area=11.22 rise=3.44 twist=29.1
  strand#1  U DNA glyco-bond=s-- nts=3 GGG A.DG1,A.DG2,A.DG3
  strand#2  U DNA glyco-bond=s-- nts=3 GgG A.DG14,A.GFL15,A.DG16
  strand#3  D DNA glyco-bond=-ss nts=3 GGG A.DG22,A.DG21,A.DG20
  strand#4  D DNA glyco-bond=-ss nts=3 GGG A.DG8,A.DG7,A.DG6
  loop#1 type=lateral   strands=[#1,#4] nts=2 AT A.DA4,A.DT5
  loop#2 type=diagonal  strands=[#4,#2] nts=5 ACACA A.DA9,A.DC10,A.DA11,A.DC12,A.DA13
  loop#3 type=lateral   strands=[#2,#3] nts=3 GAC A.DG17,A.DA18,A.DC19

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List of 0 G4 coaxial stacks [summary · schematics · tetrads · helices · stems · homepage]

List of 0 non-stem G4-loops (including the two closing Gs)