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

PDB-id
1s9l
Class
RNA
Method
NMR
Summary
NMR solution structure of a parallel lna quadruplex
Reference
Randazzo, A., Esposito, V., Ohlenschlager, O., Ramachandran, R., Mayola, L.: (2004) "NMR solution structure of a parallel LNA quadruplex." Nucleic Acids Res., 32, 3083-3092.
Abstract
The solution structure of a locked nucleic acid (LNA) quadruplex, formed by the oligomer d(TGGGT), containing only conformationally restricted LNA residues is reported. NMR and CD spectroscopy, as well as molecular dynamics and mechanic calculations, has been used to characterize the complex. The molecule adopts a parallel stranded conformation with a 4-fold rotational symmetry, showing a right-handed helicity and the guanine residues in an almost planar conformation with three well-defined G-tetrads. The thermal stability of Q-LNA has been found to be comparable with that of [r(UGGGU)]4, while a T(m) increment of 20 degrees C with respect to the corresponding DNA quadruplex structure [d(TGGGT)]4 has been observed. The structural features of the LNA quadruplex reported here may open new perspectives for the biological application of LNAs as novel versatile tools to design aptamer or catalyst oligonucleotides.
G4 notes
3 G-tetrads, 1 G4 helix, 1 G4 stem · parallel(4+0), UUUU

Base-block schematics in six views [summary · tetrads · helices · stems · costacks · homepage]

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List of 3 G-tetrads [summary · schematics · helices · stems · costacks · homepage]

 1 glyco-bond=---- groove=---- planarity=0.227 type=other  nts=4 gggg A.LCG2,C.LCG12,D.LCG17,B.LCG7
 2 glyco-bond=---- groove=---- planarity=0.208 type=other  nts=4 gggg A.LCG3,C.LCG13,D.LCG18,B.LCG8
 3 glyco-bond=---- groove=---- planarity=0.191 type=other  nts=4 gggg A.LCG4,C.LCG14,D.LCG19,B.LCG9

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, inter-molecular, with 1 stem

 1  glyco-bond=---- groove=---- WC-->Major nts=4 gggg A.LCG2,C.LCG12,D.LCG17,B.LCG7
 2  glyco-bond=---- groove=---- WC-->Major nts=4 gggg A.LCG3,C.LCG13,D.LCG18,B.LCG8
 3  glyco-bond=---- groove=---- WC-->Major nts=4 gggg A.LCG4,C.LCG14,D.LCG19,B.LCG9
  step#1  pm(>>,forward)  area=15.69 rise=3.49 twist=28.9
  step#2  pm(>>,forward)  area=15.90 rise=3.49 twist=27.8
  strand#1 ... glyco-bond=--- nts=3 ggg A.LCG2,A.LCG3,A.LCG4
  strand#2 ... glyco-bond=--- nts=3 ggg C.LCG12,C.LCG13,C.LCG14
  strand#3 ... glyco-bond=--- nts=3 ggg D.LCG17,D.LCG18,D.LCG19
  strand#4 ... glyco-bond=--- nts=3 ggg B.LCG7,B.LCG8,B.LCG9

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2 stacking diagrams
 1  glyco-bond=---- groove=---- WC-->Major nts=4 gggg A.LCG2,C.LCG12,D.LCG17,B.LCG7
2 glyco-bond=---- groove=---- WC-->Major nts=4 gggg A.LCG3,C.LCG13,D.LCG18,B.LCG8
step#1 pm(>>,forward) area=15.69 rise=3.49 twist=28.9

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 2  glyco-bond=---- groove=---- WC-->Major nts=4 gggg A.LCG3,C.LCG13,D.LCG18,B.LCG8
3 glyco-bond=---- groove=---- WC-->Major nts=4 gggg A.LCG4,C.LCG14,D.LCG19,B.LCG9
step#2 pm(>>,forward) area=15.90 rise=3.49 twist=27.8

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

 1  glyco-bond=---- groove=---- WC-->Major nts=4 gggg A.LCG2,C.LCG12,D.LCG17,B.LCG7
 2  glyco-bond=---- groove=---- WC-->Major nts=4 gggg A.LCG3,C.LCG13,D.LCG18,B.LCG8
 3  glyco-bond=---- groove=---- WC-->Major nts=4 gggg A.LCG4,C.LCG14,D.LCG19,B.LCG9
  step#1  pm(>>,forward)  area=15.69 rise=3.49 twist=28.9
  step#2  pm(>>,forward)  area=15.90 rise=3.49 twist=27.8
  strand#1  U ... glyco-bond=--- nts=3 ggg A.LCG2,A.LCG3,A.LCG4
  strand#2  U ... glyco-bond=--- nts=3 ggg C.LCG12,C.LCG13,C.LCG14
  strand#3  U ... glyco-bond=--- nts=3 ggg D.LCG17,D.LCG18,D.LCG19
  strand#4  U ... glyco-bond=--- nts=3 ggg B.LCG7,B.LCG8,B.LCG9

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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)