Summary information

PDB id
2wcn
Class
DNA
Method
NMR
Summary
Solution structure of an lna-modified quadruplex
Reference
Nielsen JT, Arar K, Petersen M (2009): "Solution Structure of a Locked Nucleic Acid Modified Quadruplex: Introducing the V4 Folding Topology." Angew.Chem.Int.Ed.Engl., 48, 3099. doi: 10.1002/ANIE.200806244.
Abstract
Sharp curves: The structure of a locked nucleic acid modified telomeric sequence from Oxytricha nova displays a remarkable folding topology, distinct from the native O. nova quadruplex. Each guanine stretch folds back in a V-shaped turn that puts the first and fourth guanines in the same tetrad, looping over a tetrad with a sharp turn in the DNA backbone, showing how subtle interplay between sequence and conformation defines the folding topology.
G4 notes
4 G-tetrads, 1 G4 helix, 1 G4 stem, (2+2), UDUD

Base-block schematics in six views

PyMOL session file PDB file View in 3Dmol.js

List of 4 G-tetrads

 1 glyco-bond=s-s- sugar=3333 groove=wnwn planarity=0.137 type=planar nts=4 GgGg A.DG1,A.LCG12,A.DG9,A.LCG4
 2 glyco-bond=---- sugar=3-3- groove=---- planarity=0.100 type=planar nts=4 gGgG A.LCG2,B.DG23,A.LCG10,B.DG15
 3 glyco-bond=---- sugar=-3-3 groove=---- planarity=0.093 type=planar nts=4 GgGg A.DG3,B.LCG14,A.DG11,B.LCG22
 4 glyco-bond=s-s- sugar=3333 groove=wnwn planarity=0.151 type=planar nts=4 GgGg B.DG13,B.LCG24,B.DG21,B.LCG16

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, 4 G-tetrad layers, inter-molecular, with 1 stem

 1  glyco-bond=s-s- sugar=3333 groove=wnwn Major-->WC nts=4 GgGg A.DG1,A.LCG12,A.DG9,A.LCG4
 2  glyco-bond=---- sugar=3-3- groove=---- Major-->WC nts=4 gGgG B.LCG22,A.DG11,B.LCG14,A.DG3
 3  glyco-bond=---- sugar=-3-3 groove=---- WC-->Major nts=4 GgGg B.DG23,A.LCG10,B.DG15,A.LCG2
 4  glyco-bond=-s-s sugar=3333 groove=wnwn WC-->Major nts=4 gGgG B.LCG24,B.DG13,B.LCG16,B.DG21
  step#1  mp(<<,backward) area=10.50 rise=3.21 twist=32.8
  step#2  mm(<>,outward)  area=12.95 rise=3.33 twist=43.4
  step#3  pm(>>,forward)  area=10.52 rise=3.21 twist=32.8
  strand#1 DNA glyco-bond=s--- sugar=33-3 nts=4 GgGg A.DG1,B.LCG22,B.DG23,B.LCG24
  strand#2 DNA glyco-bond=---s sugar=3-33 nts=4 gGgG A.LCG12,A.DG11,A.LCG10,B.DG13
  strand#3 DNA glyco-bond=s--- sugar=33-3 nts=4 GgGg A.DG9,B.LCG14,B.DG15,B.LCG16
  strand#4 DNA glyco-bond=---s sugar=3-33 nts=4 gGgG A.LCG4,A.DG3,A.LCG2,B.DG21

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3 stacking diagrams 
 1  glyco-bond=s-s- sugar=3333 groove=wnwn Major-->WC nts=4 GgGg A.DG1,A.LCG12,A.DG9,A.LCG4
 2  glyco-bond=---- sugar=3-3- groove=---- Major-->WC nts=4 gGgG B.LCG22,A.DG11,B.LCG14,A.DG3
  step#1  mp(<<,backward) area=10.50 rise=3.21 twist=32.8

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 2  glyco-bond=---- sugar=3-3- groove=---- Major-->WC nts=4 gGgG B.LCG22,A.DG11,B.LCG14,A.DG3
 3  glyco-bond=---- sugar=-3-3 groove=---- WC-->Major nts=4 GgGg B.DG23,A.LCG10,B.DG15,A.LCG2
  step#2  mm(<>,outward)  area=12.95 rise=3.33 twist=43.4

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 3  glyco-bond=---- sugar=-3-3 groove=---- WC-->Major nts=4 GgGg B.DG23,A.LCG10,B.DG15,A.LCG2
 4  glyco-bond=-s-s sugar=3333 groove=wnwn WC-->Major nts=4 gGgG B.LCG24,B.DG13,B.LCG16,B.DG21
  step#3  pm(>>,forward)  area=10.52 rise=3.21 twist=32.8

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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, 2 G-tetrad layers, 2 loops, inter-molecular, UDUD, anti-parallel, (2+2)

 1  glyco-bond=---- sugar=3-3- groove=---- Major-->WC nts=4 gGgG A.LCG2,B.DG15,A.LCG10,B.DG23
 2  glyco-bond=---- sugar=-3-3 groove=---- WC-->Major nts=4 GgGg A.DG3,B.LCG14,A.DG11,B.LCG22
  step#1  mm(<>,outward)  area=12.95 rise=3.33 twist=43.4
  strand#1  U DNA glyco-bond=-- sugar=3- nts=2 gG A.LCG2,A.DG3
  strand#2  D DNA glyco-bond=-- sugar=-3 nts=2 Gg B.DG15,B.LCG14
  strand#3  U DNA glyco-bond=-- sugar=3- nts=2 gG A.LCG10,A.DG11
  strand#4  D DNA glyco-bond=-- sugar=-3 nts=2 Gg B.DG23,B.LCG22
  loop#1 type=diag-prop strands=[#1,#3] nts=6 gTTTTG A.LCG4,A.DT5,A.DT6,A.DT7,A.DT8,A.DG9
  loop#2 type=diag-prop strands=[#2,#4] nts=6 gTTTTG B.LCG16,B.DT17,B.DT18,B.DT19,B.DT20,B.DG21

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List of 6 non-stem G4-loops (including the two closing Gs)

 1 type=V-shaped  helix=#1 nts=4 GgGg A.DG1,A.LCG2,A.DG3,A.LCG4
 2 type=lateral   helix=#1 nts=6 gTTTTG A.LCG4,A.DT5,A.DT6,A.DT7,A.DT8,A.DG9
 3 type=V-shaped  helix=#1 nts=4 GgGg A.DG9,A.LCG10,A.DG11,A.LCG12
 4 type=V-shaped  helix=#1 nts=4 GgGg B.DG13,B.LCG14,B.DG15,B.LCG16
 5 type=lateral   helix=#1 nts=6 gTTTTG B.LCG16,B.DT17,B.DT18,B.DT19,B.DT20,B.DG21
 6 type=V-shaped  helix=#1 nts=4 GgGg B.DG21,B.LCG22,B.DG23,B.LCG24