Summary information and primary citation

PDB-id
9k70
Class
DNA-RNA hybrid
Method
NMR
Summary
A (3+1) hybrid g-quadruplex assembled between two strands of human telomeric DNA and RNA
Reference
Fu WQ, Zhang N: "Guanine ribonucleotide atypically adaptive to syn glycosidic conformation in an RNA-DNA hybrid G-quadruplex with topologically (3+1) mixed strand orientation."
Abstract
 
G4 notes
3 G-tetrads, 1 G4 helix, 1 G4 stem, UDUU, hybrid3, 3+1

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

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List of 3 G-tetrads

 1 glyco-bond=s-ss sugar=---- groove=wn-- planarity=0.261 type=other  -- nts=4 GGGG A.DG1,A.DG9,A.DG13,B.G23
 2 glyco-bond=-s-- sugar=---- groove=wn-- planarity=0.271 type=other  -- nts=4 GGGG A.DG2,A.DG8,A.DG14,B.G24
 3 glyco-bond=-s-- sugar=---3 groove=wn-- planarity=0.017 type=planar -- nts=4 GGGG A.DG3,A.DG7,A.DG15,B.G25

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-tetrads, inter-molecular, with 1 stem
 1  glyco-bond=s-ss sugar=---- groove=wn-- Major-->WC -- nts=4 GGGG A.DG1,A.DG9,A.DG13,B.G23
 2  glyco-bond=-s-- sugar=---- groove=wn-- WC-->Major -- nts=4 GGGG A.DG2,A.DG8,A.DG14,B.G24
 3  glyco-bond=-s-- sugar=---3 groove=wn-- WC-->Major -- nts=4 GGGG A.DG3,A.DG7,A.DG15,B.G25
  step#1  mm(<>,outward)  area=15.34 rise=4.26 twist=20.2
  step#2  pm(>>,forward)  area=13.33 rise=3.72 twist=27.1
  strand#1 DNA glyco-bond=s-- sugar=--- nts=3 GGG A.DG1,A.DG2,A.DG3
  strand#2 DNA glyco-bond=-ss sugar=--- nts=3 GGG A.DG9,A.DG8,A.DG7
  strand#3 DNA glyco-bond=s-- sugar=--- nts=3 GGG A.DG13,A.DG14,A.DG15
  strand#4 RNA glyco-bond=s-- sugar=--3 nts=3 GGG B.G23,B.G24,B.G25

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2 stacking diagrams 
 1  glyco-bond=s-ss sugar=---- groove=wn-- Major-->WC -- nts=4 GGGG A.DG1,A.DG9,A.DG13,B.G23
 2  glyco-bond=-s-- sugar=---- groove=wn-- WC-->Major -- nts=4 GGGG A.DG2,A.DG8,A.DG14,B.G24
  step#1  mm(<>,outward)  area=15.34 rise=4.26 twist=20.2

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 2  glyco-bond=-s-- sugar=---- groove=wn-- WC-->Major -- nts=4 GGGG A.DG2,A.DG8,A.DG14,B.G24
 3  glyco-bond=-s-- sugar=---3 groove=wn-- WC-->Major -- nts=4 GGGG A.DG3,A.DG7,A.DG15,B.G25
  step#2  pm(>>,forward)  area=13.33 rise=3.72 twist=27.1

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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-tetrads, 2 loops, inter-molecular, UDUU, hybrid3, 3+1
 1  glyco-bond=s-ss sugar=---- groove=wn-- Major-->WC -- nts=4 GGGG A.DG1,A.DG9,A.DG13,B.G23
 2  glyco-bond=-s-- sugar=---- groove=wn-- WC-->Major -- nts=4 GGGG A.DG2,A.DG8,A.DG14,B.G24
 3  glyco-bond=-s-- sugar=---3 groove=wn-- WC-->Major -- nts=4 GGGG A.DG3,A.DG7,A.DG15,B.G25
  step#1  mm(<>,outward)  area=15.34 rise=4.26 twist=20.2
  step#2  pm(>>,forward)  area=13.33 rise=3.72 twist=27.1
  strand#1  U DNA glyco-bond=s-- sugar=--- nts=3 GGG A.DG1,A.DG2,A.DG3
  strand#2  D DNA glyco-bond=-ss sugar=--- nts=3 GGG A.DG9,A.DG8,A.DG7
  strand#3  U DNA glyco-bond=s-- sugar=--- nts=3 GGG A.DG13,A.DG14,A.DG15
  strand#4  U RNA glyco-bond=s-- sugar=--3 nts=3 GGG B.G23,B.G24,B.G25
  loop#1 type=lateral   strands=[#1,#2] nts=3 TTA A.DT4,A.DT5,A.DA6
  loop#2 type=lateral   strands=[#2,#3] nts=3 TTA A.DT10,A.DT11,A.DA12

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