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

PDB-id
2chk
Class
nucleic acid
Method
NMR
Summary
NMR structure of tllllt quadruplex
Reference
Nielsen, J.T., Arar, K., Petersen, M.: (2006) "NMR Solution Structures of Lna (Locked Nucleic Acid) Modified Quadruplexes." Nucleic Acids Res., 34, 2006-.
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 [summary · tetrads · helices · stems · costacks · homepage]

PyMOL session file PDB file View in 3Dmol.js

List of 4 G-tetrads [summary · schematics · helices · stems · costacks · homepage]

 1 glyco-bond=---- groove=---- planarity=0.514 type=other  nts=4 gggg A.LCG2,B.LCG8,C.LCG14,D.LCG20
 2 glyco-bond=---- groove=---- planarity=0.350 type=other  nts=4 gggg A.LCG3,B.LCG9,C.LCG15,D.LCG21
 3 glyco-bond=---- groove=---- planarity=0.212 type=other  nts=4 gggg A.LCG4,B.LCG10,C.LCG16,D.LCG22
 4 glyco-bond=---- groove=---- planarity=0.164 type=other  nts=4 gggg A.LCG5,B.LCG11,C.LCG17,D.LCG23

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

 1  glyco-bond=---- groove=---- WC-->Major nts=4 gggg A.LCG2,B.LCG8,C.LCG14,D.LCG20
 2  glyco-bond=---- groove=---- WC-->Major nts=4 gggg A.LCG3,B.LCG9,C.LCG15,D.LCG21
 3  glyco-bond=---- groove=---- WC-->Major nts=4 gggg A.LCG4,B.LCG10,C.LCG16,D.LCG22
 4  glyco-bond=---- groove=---- WC-->Major nts=4 gggg A.LCG5,B.LCG11,C.LCG17,D.LCG23
  step#1  pm(>>,forward)  area=14.32 rise=3.65 twist=24.9
  step#2  pm(>>,forward)  area=15.11 rise=3.69 twist=24.6
  step#3  pm(>>,forward)  area=13.93 rise=3.44 twist=28.8
  strand#1 ... glyco-bond=---- nts=4 gggg A.LCG2,A.LCG3,A.LCG4,A.LCG5
  strand#2 ... glyco-bond=---- nts=4 gggg B.LCG8,B.LCG9,B.LCG10,B.LCG11
  strand#3 ... glyco-bond=---- nts=4 gggg C.LCG14,C.LCG15,C.LCG16,C.LCG17
  strand#4 ... glyco-bond=---- nts=4 gggg D.LCG20,D.LCG21,D.LCG22,D.LCG23

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3 stacking diagrams
 1  glyco-bond=---- groove=---- WC-->Major nts=4 gggg A.LCG2,B.LCG8,C.LCG14,D.LCG20
2 glyco-bond=---- groove=---- WC-->Major nts=4 gggg A.LCG3,B.LCG9,C.LCG15,D.LCG21
step#1 pm(>>,forward) area=14.32 rise=3.65 twist=24.9

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 2  glyco-bond=---- groove=---- WC-->Major nts=4 gggg A.LCG3,B.LCG9,C.LCG15,D.LCG21
3 glyco-bond=---- groove=---- WC-->Major nts=4 gggg A.LCG4,B.LCG10,C.LCG16,D.LCG22
step#2 pm(>>,forward) area=15.11 rise=3.69 twist=24.6

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 3  glyco-bond=---- groove=---- WC-->Major nts=4 gggg A.LCG4,B.LCG10,C.LCG16,D.LCG22
4 glyco-bond=---- groove=---- WC-->Major nts=4 gggg A.LCG5,B.LCG11,C.LCG17,D.LCG23
step#3 pm(>>,forward) area=13.93 rise=3.44 twist=28.8

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

 1  glyco-bond=---- groove=---- WC-->Major nts=4 gggg A.LCG2,B.LCG8,C.LCG14,D.LCG20
 2  glyco-bond=---- groove=---- WC-->Major nts=4 gggg A.LCG3,B.LCG9,C.LCG15,D.LCG21
 3  glyco-bond=---- groove=---- WC-->Major nts=4 gggg A.LCG4,B.LCG10,C.LCG16,D.LCG22
 4  glyco-bond=---- groove=---- WC-->Major nts=4 gggg A.LCG5,B.LCG11,C.LCG17,D.LCG23
  step#1  pm(>>,forward)  area=14.32 rise=3.65 twist=24.9
  step#2  pm(>>,forward)  area=15.11 rise=3.69 twist=24.6
  step#3  pm(>>,forward)  area=13.93 rise=3.44 twist=28.8
  strand#1  U ... glyco-bond=---- nts=4 gggg A.LCG2,A.LCG3,A.LCG4,A.LCG5
  strand#2  U ... glyco-bond=---- nts=4 gggg B.LCG8,B.LCG9,B.LCG10,B.LCG11
  strand#3  U ... glyco-bond=---- nts=4 gggg C.LCG14,C.LCG15,C.LCG16,C.LCG17
  strand#4  U ... glyco-bond=---- nts=4 gggg D.LCG20,D.LCG21,D.LCG22,D.LCG23

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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)