Summary information and primary citation

PDB-id
9whv
Class
RNA
Method
NMR
Summary
Cross-stacking-stabilized intra-locked RNA g-quadruplex
Reference
Song SS, Yang L, Wang LW, Tian RQ, Wang SY, Jia MH, Xu Y, Zhong MQ, Liang XG, Hu KL, Luo H, Chen Y, Hu XX, Shen XC, Xiao CD (2026): "An intra-locked RNA G-quadruplex topology confers enhanced nuclease resistance and cancer cell targeting." Int.J.Biol.Macromol., 367, 152564. doi: 10.1016/j.ijbiomac.2026.152564.
Abstract
 
G4 notes
6 G-tetrads, 2 G4 helices, 2 G4 stems, UUUU, parallel, 4+0

Cartoon-block schematics in six views (download the tarball)

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List of 6 G-tetrads

 1 glyco-bond=---- sugar=33.3 groove=---- planarity=0.167 type=other  -- nts=4 GGGG A.G1,D.G1,C.G1,B.G1
 2 glyco-bond=---- sugar=---- groove=---- planarity=0.185 type=other  -- nts=4 GGGG A.G5,D.G5,C.G5,B.G5
 3 glyco-bond=---- sugar=---- groove=---- planarity=0.175 type=other  -- nts=4 GGGG A.G6,D.G6,C.G6,B.G6
 4 glyco-bond=---- sugar=33.3 groove=---- planarity=0.129 type=planar -- nts=4 GGGG E.G1,H.G1,G.G1,F.G1
 5 glyco-bond=---- sugar=---- groove=---- planarity=0.244 type=other  -- nts=4 GGGG E.G6,H.G6,G.G6,F.G6
 6 glyco-bond=---- sugar=.--. groove=---- planarity=0.136 type=planar -- nts=4 GGGG E.G7,H.G7,G.G7,F.G7

List of 2 G4-helices

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-tetrads, inter-molecular, with 1 stem
 1  glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG A.G6,D.G6,C.G6,B.G6
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG A.G5,D.G5,C.G5,B.G5
 3  glyco-bond=---- sugar=33.3 groove=---- Major-->WC -- nts=4 GGGG E.G1,F.G1,G.G1,H.G1
  step#1  mp(<<,backward) area=12.25 rise=3.01 twist=28.9
  step#2  mm(<>,outward)  area=0.00  rise=6.44 twist=-5.7
  strand#1 RNA glyco-bond=--- sugar=--3 nts=3 GGG A.G6,A.G5,E.G1
  strand#2 RNA glyco-bond=--- sugar=--3 nts=3 GGG D.G6,D.G5,F.G1
  strand#3 RNA glyco-bond=--- sugar=--. nts=3 GGG C.G6,C.G5,G.G1
  strand#4 RNA glyco-bond=--- sugar=--3 nts=3 GGG B.G6,B.G5,H.G1

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2 stacking diagrams 
 1  glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG A.G6,D.G6,C.G6,B.G6
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG A.G5,D.G5,C.G5,B.G5
  step#1  mp(<<,backward) area=12.25 rise=3.01 twist=28.9

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 2  glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG A.G5,D.G5,C.G5,B.G5
 3  glyco-bond=---- sugar=33.3 groove=---- Major-->WC -- nts=4 GGGG E.G1,F.G1,G.G1,H.G1
  step#2  mm(<>,outward)  area=0.00  rise=6.44 twist=-5.7

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Helix#2, 2 G-tetrads, inter-molecular, with 1 stem
 1  glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG E.G6,H.G6,G.G6,F.G6
 2  glyco-bond=---- sugar=.--. groove=---- WC-->Major -- nts=4 GGGG E.G7,H.G7,G.G7,F.G7
  step#1  pm(>>,forward)  area=7.72  rise=3.10 twist=34.0
  strand#1 RNA glyco-bond=-- sugar=-. nts=2 GG E.G6,E.G7
  strand#2 RNA glyco-bond=-- sugar=-- nts=2 GG H.G6,H.G7
  strand#3 RNA glyco-bond=-- sugar=-- nts=2 GG G.G6,G.G7
  strand#4 RNA glyco-bond=-- sugar=-. nts=2 GG F.G6,F.G7

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1 stacking diagram 
 1  glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG E.G6,H.G6,G.G6,F.G6
 2  glyco-bond=---- sugar=.--. groove=---- WC-->Major -- nts=4 GGGG E.G7,H.G7,G.G7,F.G7
  step#1  pm(>>,forward)  area=7.72  rise=3.10 twist=34.0

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List of 2 G4-stems

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-tetrads, 0 loops, inter-molecular, UUUU, parallel, 4+0
 1  glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG A.G5,D.G5,C.G5,B.G5
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG A.G6,D.G6,C.G6,B.G6
  step#1  pm(>>,forward)  area=12.25 rise=3.01 twist=28.9
  strand#1  U RNA glyco-bond=-- sugar=-- nts=2 GG A.G5,A.G6
  strand#2  U RNA glyco-bond=-- sugar=-- nts=2 GG D.G5,D.G6
  strand#3  U RNA glyco-bond=-- sugar=-- nts=2 GG C.G5,C.G6
  strand#4  U RNA glyco-bond=-- sugar=-- nts=2 GG B.G5,B.G6

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Stem#2, 2 G-tetrads, 0 loops, inter-molecular, UUUU, parallel, 4+0
 1  glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG E.G6,H.G6,G.G6,F.G6
 2  glyco-bond=---- sugar=.--. groove=---- WC-->Major -- nts=4 GGGG E.G7,H.G7,G.G7,F.G7
  step#1  pm(>>,forward)  area=7.72  rise=3.10 twist=34.0
  strand#1  U RNA glyco-bond=-- sugar=-. nts=2 GG E.G6,E.G7
  strand#2  U RNA glyco-bond=-- sugar=-- nts=2 GG H.G6,H.G7
  strand#3  U RNA glyco-bond=-- sugar=-- nts=2 GG G.G6,G.G7
  strand#4  U RNA glyco-bond=-- sugar=-. nts=2 GG F.G6,F.G7

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