Summary information

PDB id
2chj
Class
nucleic acid
Method
NMR
Summary
NMR structure of tglglt quadruplex
Reference
Nielsen JT, Arar K, Petersen M (2006): "NMR Solution Structures of Lna (Locked Nucleic Acid) Modified Quadruplexes." Nucleic Acids Res., 34, 2006. doi: 10.1093/NAR/GKL144.
Abstract
We have determined the NMR solution structures of the quadruplexes formed by d(TGLGLT) and d(TL4T), where L denotes LNA (locked nucleic acid) modified G-residues. Both structures are tetrameric, parallel and right-handed and the native global fold of the corresponding DNA quadruplex is retained upon introduction of the LNA nucleotides. However, local structural alterations are observed owing to the locked LNA sugars. In particular, a distinct change in the sugar-phosphate backbone is observed at the G2pL3 and L2pL3 base steps and sequence dependent changes in the twist between tetrads are also seen. Both the LNA modified quadruplexes have raised thermostability as compared to the DNA quadruplex. The quadruplex-forming capability of d(TGLGLT) is of particular interest as it expands the design flexibility for stable parallel LNA quadruplexes and shows that LNA nucleotides can be mixed with DNA or other modified nucleic acids. As such, LNA-based quadruplexes can be decorated by a variety of chemical modifications. Such LNA quadruplex scaffolds might find applications in the developing field of nanobiotechnology.
G4 notes
4 G-tetrads, 1 G4 helix, 1 G4 stem, parallel(4+0), UUUU

Base-block schematics in six views

PyMOL session file PDB file View in 3Dmol.js

List of 4 G-tetrads

 1 glyco-bond=---- sugar=---- groove=---- planarity=0.281 type=other  nts=4 GGGG A.DG2,B.DG8,C.DG14,D.DG20
 2 glyco-bond=---- sugar=3333 groove=---- planarity=0.313 type=other  nts=4 gggg A.LCG3,B.LCG9,C.LCG15,D.LCG21
 3 glyco-bond=---- sugar=3333 groove=---- planarity=0.118 type=planar nts=4 GGGG A.DG4,B.DG10,C.DG16,D.DG22
 4 glyco-bond=---- sugar=3333 groove=---- planarity=0.241 type=other  nts=4 gggg A.LCG5,B.LCG11,C.LCG17,D.LCG23

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=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG2,B.DG8,C.DG14,D.DG20
 2  glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 gggg A.LCG3,B.LCG9,C.LCG15,D.LCG21
 3  glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG A.DG4,B.DG10,C.DG16,D.DG22
 4  glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 gggg A.LCG5,B.LCG11,C.LCG17,D.LCG23
  step#1  pm(>>,forward)  area=23.67 rise=3.31 twist=21.1
  step#2  pm(>>,forward)  area=9.60  rise=3.40 twist=32.3
  step#3  pm(>>,forward)  area=18.59 rise=3.38 twist=22.7
  strand#1 DNA glyco-bond=---- sugar=-333 nts=4 GgGg A.DG2,A.LCG3,A.DG4,A.LCG5
  strand#2 DNA glyco-bond=---- sugar=-333 nts=4 GgGg B.DG8,B.LCG9,B.DG10,B.LCG11
  strand#3 DNA glyco-bond=---- sugar=-333 nts=4 GgGg C.DG14,C.LCG15,C.DG16,C.LCG17
  strand#4 DNA glyco-bond=---- sugar=-333 nts=4 GgGg D.DG20,D.LCG21,D.DG22,D.LCG23

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3 stacking diagrams 
 1  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG2,B.DG8,C.DG14,D.DG20
 2  glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 gggg A.LCG3,B.LCG9,C.LCG15,D.LCG21
  step#1  pm(>>,forward)  area=23.67 rise=3.31 twist=21.1

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 2  glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 gggg A.LCG3,B.LCG9,C.LCG15,D.LCG21
 3  glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG A.DG4,B.DG10,C.DG16,D.DG22
  step#2  pm(>>,forward)  area=9.60  rise=3.40 twist=32.3

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 3  glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG A.DG4,B.DG10,C.DG16,D.DG22
 4  glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 gggg A.LCG5,B.LCG11,C.LCG17,D.LCG23
  step#3  pm(>>,forward)  area=18.59 rise=3.38 twist=22.7

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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, 4 G-tetrad layers, 0 loops, inter-molecular, UUUU, parallel, parallel(4+0)

 1  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG2,B.DG8,C.DG14,D.DG20
 2  glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 gggg A.LCG3,B.LCG9,C.LCG15,D.LCG21
 3  glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG A.DG4,B.DG10,C.DG16,D.DG22
 4  glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 gggg A.LCG5,B.LCG11,C.LCG17,D.LCG23
  step#1  pm(>>,forward)  area=23.67 rise=3.31 twist=21.1
  step#2  pm(>>,forward)  area=9.60  rise=3.40 twist=32.3
  step#3  pm(>>,forward)  area=18.59 rise=3.38 twist=22.7
  strand#1  U DNA glyco-bond=---- sugar=-333 nts=4 GgGg A.DG2,A.LCG3,A.DG4,A.LCG5
  strand#2  U DNA glyco-bond=---- sugar=-333 nts=4 GgGg B.DG8,B.LCG9,B.DG10,B.LCG11
  strand#3  U DNA glyco-bond=---- sugar=-333 nts=4 GgGg C.DG14,C.LCG15,C.DG16,C.LCG17
  strand#4  U DNA glyco-bond=---- sugar=-333 nts=4 GgGg D.DG20,D.LCG21,D.DG22,D.LCG23

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