Summary information

PDB id
7o1h
Class
DNA
Method
NMR
Summary
Hybrid-2r quadruplex-duplex with (-p-p-l) topology and 3 syn residues
Reference
Mohr S, Jana J, Vianney YM, Weisz K (2021): "Expanding the Topological Landscape by a G-Column Flip of a Parallel G-Quadruplex." Chemistry, 27, 10437-10447. doi: 10.1002/chem.202101181.
Abstract
Canonical G-quadruplexes can adopt a variety of different topologies depending on the arrangement of propeller, lateral, or diagonal loops connecting the four G-columns. A novel intramolecular G-quadruplex structure is derived through inversion of the last G-tract of a three-layered parallel fold, associated with the transition of a single propeller into a lateral loop. The resulting (3+1) hybrid fold features three syn·anti·anti·anti G-tetrads with a 3'-terminal all- syn G-column. Although the ability of forming a duplex stem-loop between G-tracts seems beneficial for a propeller-to-lateral loop rearrangement, unmodified G-rich sequences resist folding into the new (3+1) topology. However, refolding can be driven by the incorporation of syn -favoring guanosine analogs into positions of the fourth G-stretch. The presented hybrid-type G-quadruplex structure as determined by NMR may provide for an additional scaffold in quadruplex-based technologies.
G4 notes
3 G-tetrads, 1 G4 helix, 1 G4 stem, 3(-P-P-Lw), hybrid-2R(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=0.160 type=planar nts=4 GGGg A.DG4,A.DG8,A.DG12,A.BGM28
 2 glyco-bond=---s sugar=--.- groove=--wn planarity=0.088 type=planar nts=4 GGGG A.DG5,A.DG9,A.DG13,A.DG27
 3 glyco-bond=---s sugar=---- groove=--wn planarity=0.145 type=planar nts=4 GGGg A.DG6,A.DG10,A.DG14,A.BGM26

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 A.DG4,A.DG8,A.DG12,A.BGM28
 2  glyco-bond=---s sugar=--.- groove=--wn WC-->Major nts=4 GGGG A.DG5,A.DG9,A.DG13,A.DG27
 3  glyco-bond=---s sugar=---- groove=--wn WC-->Major nts=4 GGGg A.DG6,A.DG10,A.DG14,A.BGM26
  step#1  pm(>>,forward)  area=13.57 rise=3.39 twist=26.7
  step#2  pm(>>,forward)  area=12.00 rise=3.44 twist=28.4
  strand#1 DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG4,A.DG5,A.DG6
  strand#2 DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG8,A.DG9,A.DG10
  strand#3 DNA glyco-bond=--- sugar=-.- nts=3 GGG A.DG12,A.DG13,A.DG14
  strand#4 DNA glyco-bond=sss sugar=.-- nts=3 gGg A.BGM28,A.DG27,A.BGM26

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2 stacking diagrams 
 1  glyco-bond=---s sugar=---. groove=--wn WC-->Major nts=4 GGGg A.DG4,A.DG8,A.DG12,A.BGM28
 2  glyco-bond=---s sugar=--.- groove=--wn WC-->Major nts=4 GGGG A.DG5,A.DG9,A.DG13,A.DG27
  step#1  pm(>>,forward)  area=13.57 rise=3.39 twist=26.7

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 2  glyco-bond=---s sugar=--.- groove=--wn WC-->Major nts=4 GGGG A.DG5,A.DG9,A.DG13,A.DG27
 3  glyco-bond=---s sugar=---- groove=--wn WC-->Major nts=4 GGGg A.DG6,A.DG10,A.DG14,A.BGM26
  step#2  pm(>>,forward)  area=12.00 rise=3.44 twist=28.4

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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(-P-P-Lw), hybrid-2R(3+1)

 1  glyco-bond=---s sugar=---. groove=--wn WC-->Major nts=4 GGGg A.DG4,A.DG8,A.DG12,A.BGM28
 2  glyco-bond=---s sugar=--.- groove=--wn WC-->Major nts=4 GGGG A.DG5,A.DG9,A.DG13,A.DG27
 3  glyco-bond=---s sugar=---- groove=--wn WC-->Major nts=4 GGGg A.DG6,A.DG10,A.DG14,A.BGM26
  step#1  pm(>>,forward)  area=13.57 rise=3.39 twist=26.7
  step#2  pm(>>,forward)  area=12.00 rise=3.44 twist=28.4
  strand#1  U DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG4,A.DG5,A.DG6
  strand#2  U DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG8,A.DG9,A.DG10
  strand#3  U DNA glyco-bond=--- sugar=-.- nts=3 GGG A.DG12,A.DG13,A.DG14
  strand#4  D DNA glyco-bond=sss sugar=.-- nts=3 gGg A.BGM28,A.DG27,A.BGM26
  loop#1 type=propeller strands=[#1,#2] nts=1 T A.DT7
  loop#2 type=propeller strands=[#2,#3] nts=1 T A.DT11
  loop#3 type=lateral   strands=[#3,#4] nts=11 ACGCGCAGCGT A.DA15,A.DC16,A.DG17,A.DC18,A.DG19,A.DC20,A.DA21,A.DG22,A.DC23,A.DG24,A.DT25

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