Summary information and primary citation

PDB-id
9tnr
Class
DNA
Method
NMR
Summary
L12 g-quadruplex-forming aptamer targeting hmgb1 protein
Reference
Trajkovski M, Platella C, Musumeci D, Napolitano E, Esposito CL, Catuogno S, Plavec J, Montesarchio D (2026): "Unraveling the NMR structures of G-quadruplex-forming aptamers acting as inhibitors of High Mobility Group Box 1 (HMGB1) pathological activity." Int.J.Biol.Macromol., 357, 151585. doi: 10.1016/j.ijbiomac.2026.151585.
Abstract
 
G4 notes
3 G-tetrads, 1 G4 helix, 1 G4 stem, UDUU, hybrid3, 3+1, 3(-Lw-Ln-P)

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=0.177 type=bowl-2 O- nts=4 GGGG A.DG4,A.DG12,A.DG16,A.DG22
 2 glyco-bond=-s-- sugar=---3 groove=wn-- planarity=0.141 type=planar O+ nts=4 GGGG A.DG5,A.DG11,A.DG17,A.DG23
 3 glyco-bond=-s-- sugar=---3 groove=wn-- planarity=0.259 type=other  O+ nts=4 GGGG A.DG6,A.DG10,A.DG18,A.DG24

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, INTRA-molecular, with 1 stem
 1  glyco-bond=s-ss sugar=---- groove=wn-- Major-->WC O- nts=4 GGGG A.DG4,A.DG12,A.DG16,A.DG22
 2  glyco-bond=-s-- sugar=---3 groove=wn-- WC-->Major O+ nts=4 GGGG A.DG5,A.DG11,A.DG17,A.DG23
 3  glyco-bond=-s-- sugar=---3 groove=wn-- WC-->Major O+ nts=4 GGGG A.DG6,A.DG10,A.DG18,A.DG24
  step#1  mm(<>,outward)  area=18.84 rise=3.43 twist=15.6
  step#2  pm(>>,forward)  area=12.75 rise=3.46 twist=26.5
  strand#1 DNA glyco-bond=s-- sugar=--- nts=3 GGG A.DG4,A.DG5,A.DG6
  strand#2 DNA glyco-bond=-ss sugar=--- nts=3 GGG A.DG12,A.DG11,A.DG10
  strand#3 DNA glyco-bond=s-- sugar=--- nts=3 GGG A.DG16,A.DG17,A.DG18
  strand#4 DNA glyco-bond=s-- sugar=-33 nts=3 GGG A.DG22,A.DG23,A.DG24

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2 stacking diagrams 
 1  glyco-bond=s-ss sugar=---- groove=wn-- Major-->WC O- nts=4 GGGG A.DG4,A.DG12,A.DG16,A.DG22
 2  glyco-bond=-s-- sugar=---3 groove=wn-- WC-->Major O+ nts=4 GGGG A.DG5,A.DG11,A.DG17,A.DG23
  step#1  mm(<>,outward)  area=18.84 rise=3.43 twist=15.6

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 2  glyco-bond=-s-- sugar=---3 groove=wn-- WC-->Major O+ nts=4 GGGG A.DG5,A.DG11,A.DG17,A.DG23
 3  glyco-bond=-s-- sugar=---3 groove=wn-- WC-->Major O+ nts=4 GGGG A.DG6,A.DG10,A.DG18,A.DG24
  step#2  pm(>>,forward)  area=12.75 rise=3.46 twist=26.5

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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, 3 loops, INTRA-molecular, UDUU, hybrid3, 3+1, 3(-Lw-Ln-P)
 1  glyco-bond=s-ss sugar=---- groove=wn-- Major-->WC O- nts=4 GGGG A.DG4,A.DG12,A.DG16,A.DG22
 2  glyco-bond=-s-- sugar=---3 groove=wn-- WC-->Major O+ nts=4 GGGG A.DG5,A.DG11,A.DG17,A.DG23
 3  glyco-bond=-s-- sugar=---3 groove=wn-- WC-->Major O+ nts=4 GGGG A.DG6,A.DG10,A.DG18,A.DG24
  step#1  mm(<>,outward)  area=18.84 rise=3.43 twist=15.6
  step#2  pm(>>,forward)  area=12.75 rise=3.46 twist=26.5
  strand#1  U DNA glyco-bond=s-- sugar=--- nts=3 GGG A.DG4,A.DG5,A.DG6
  strand#2  D DNA glyco-bond=-ss sugar=--- nts=3 GGG A.DG12,A.DG11,A.DG10
  strand#3  U DNA glyco-bond=s-- sugar=--- nts=3 GGG A.DG16,A.DG17,A.DG18
  strand#4  U DNA glyco-bond=s-- sugar=-33 nts=3 GGG A.DG22,A.DG23,A.DG24
  loop#1 type=lateral   strands=[#1,#2] nts=3 ATT A.DA7,A.DT8,A.DT9
  loop#2 type=lateral   strands=[#2,#3] nts=3 AAT A.DA13,A.DA14,A.DT15
  loop#3 type=propeller strands=[#3,#4] nts=3 TAT A.DT19,A.DA20,A.DT21

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