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

PDB-id
2may
Class
DNA
Method
NMR
Summary
Structure of a G-quadruplex containing a single lna modification
Reference
Li, Z., Lech, C., Adrian, M., Heddi, B., Phan, A.T.: "Engineering G4: Towards effective incorporation of locked nucleic acid into G-quadruplexes." To be published
Abstract
 
G4 notes
3 G-tetrads, 1 G4 helix, 1 G4 stem · 3(-P-Lw-Ln), hybrid-1(3+1), UUDU

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-s groove=-wn- planarity=0.171 type=other  nts=4 GGGG A.DG3,A.DG9,A.DG17,A.DG21
 2 glyco-bond=--s- groove=-wn- planarity=0.176 type=other  nts=4 gGGG A.LCG4,A.DG10,A.DG16,A.DG22
 3 glyco-bond=--s- groove=-wn- planarity=0.207 type=bowl   nts=4 GGGG A.DG5,A.DG11,A.DG15,A.DG23

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-s groove=-wn- Major-->WC nts=4 GGGG A.DG3,A.DG9,A.DG17,A.DG21
 2  glyco-bond=--s- groove=-wn- WC-->Major nts=4 gGGG A.LCG4,A.DG10,A.DG16,A.DG22
 3  glyco-bond=--s- groove=-wn- WC-->Major nts=4 GGGG A.DG5,A.DG11,A.DG15,A.DG23
  step#1  mm(<>,outward)  area=12.99 rise=3.61 twist=20.7
  step#2  pm(>>,forward)  area=12.53 rise=3.50 twist=28.0
  strand#1 DNA glyco-bond=s-- nts=3 GgG A.DG3,A.LCG4,A.DG5
  strand#2 DNA glyco-bond=s-- nts=3 GGG A.DG9,A.DG10,A.DG11
  strand#3 DNA glyco-bond=-ss nts=3 GGG A.DG17,A.DG16,A.DG15
  strand#4 DNA glyco-bond=s-- nts=3 GGG A.DG21,A.DG22,A.DG23

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2 stacking diagrams
 1  glyco-bond=ss-s groove=-wn- Major-->WC nts=4 GGGG A.DG3,A.DG9,A.DG17,A.DG21
2 glyco-bond=--s- groove=-wn- WC-->Major nts=4 gGGG A.LCG4,A.DG10,A.DG16,A.DG22
step#1 mm(<>,outward) area=12.99 rise=3.61 twist=20.7

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 2  glyco-bond=--s- groove=-wn- WC-->Major nts=4 gGGG A.LCG4,A.DG10,A.DG16,A.DG22
3 glyco-bond=--s- groove=-wn- WC-->Major nts=4 GGGG A.DG5,A.DG11,A.DG15,A.DG23
step#2 pm(>>,forward) area=12.53 rise=3.50 twist=28.0

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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, UUDU, anti-parallel, 3(-P-Lw-Ln), hybrid-1(3+1)

 1  glyco-bond=ss-s groove=-wn- Major-->WC nts=4 GGGG A.DG3,A.DG9,A.DG17,A.DG21
 2  glyco-bond=--s- groove=-wn- WC-->Major nts=4 gGGG A.LCG4,A.DG10,A.DG16,A.DG22
 3  glyco-bond=--s- groove=-wn- WC-->Major nts=4 GGGG A.DG5,A.DG11,A.DG15,A.DG23
  step#1  mm(<>,outward)  area=12.99 rise=3.61 twist=20.7
  step#2  pm(>>,forward)  area=12.53 rise=3.50 twist=28.0
  strand#1  U DNA glyco-bond=s-- nts=3 GgG A.DG3,A.LCG4,A.DG5
  strand#2  U DNA glyco-bond=s-- nts=3 GGG A.DG9,A.DG10,A.DG11
  strand#3  D DNA glyco-bond=-ss nts=3 GGG A.DG17,A.DG16,A.DG15
  strand#4  U DNA glyco-bond=s-- nts=3 GGG A.DG21,A.DG22,A.DG23
  loop#1 type=propeller strands=[#1,#2] nts=3 TTA A.DT6,A.DT7,A.DA8
  loop#2 type=lateral   strands=[#2,#3] nts=3 TTA A.DT12,A.DT13,A.DA14
  loop#3 type=lateral   strands=[#3,#4] nts=3 TTA A.DT18,A.DT19,A.DA20

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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)