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PDB-id
2m4p
Class
DNA
Method
NMR
Summary
Solution structure of an intramolecular propeller-type G-quadruplex containing a single bulge
Reference
Mukundan, V.T., Phan, A.T.: (2013) "Bulges in G-Quadruplexes: Broadening the Definition of G-Quadruplex-Forming Sequences." J.Am.Chem.Soc., 135, 5017-5028.
Abstract
We report on the first solution structure of an intramolecular G-quadruplex containing a single bulge and present evidence for extensive occurrence of bulges in different G-quadruplex contexts. The NMR solution structure of the d(TTGTGGTGGGTGGGTGGGT) sequence reveals a propeller-type parallel-stranded G-quadruplex containing three G-tetrad layers, three double-chain-reversal loops, and a bulge. All guanines participate in the formation of the G-tetrad core, despite the interruption between the first guanine and the next two guanines by a thymine, which forms a single-residue bulge and is projected out of the G-tetrad core. To provide a more general understanding about the formation of bulges within G-quadruplexes, we systematically investigated the effects of the residue type, the size, the position, and the number of bulges on the structure and stability of G-quadruplexes. The formation of bulges has also been observed in two different G-quadruplex scaffolds with different strand orientations and folding topologies. Our results show that bulges can be formed in many different situations within G-quadruplexes. While many sequences tested in this study can form stable G-quadruplex structures, all of them defy the description of sequences G3+NL1G3+NL2G3+NL3G3+, currently used in most bioinformatics searches for identifying potential G-quadruplex-forming sequences in the genomes. Broadening of this description to include the possibilities of bulge formation should allow the identification of more G-quadruplex-forming sequences which went unnoticed in the earlier searches. This study could also open the possibilities of exploiting bulges as recognition elements for interactions between G-quadruplexes and other molecules.
G4 notes
3 G-tetrads, 1 G4 helix, 1 G4 stem · 3(-P-P-P), 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=0.145 type=planar nts=4 GGGG A.DG3,A.DG8,A.DG12,A.DG16
 2 glyco-bond=---- groove=---- planarity=0.084 type=planar nts=4 GGGG A.DG5,A.DG9,A.DG13,A.DG17
 3 glyco-bond=---- groove=---- planarity=0.087 type=planar nts=4 GGGG A.DG6,A.DG10,A.DG14,A.DG18

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=---- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG8,A.DG12,A.DG16
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG5,A.DG9,A.DG13,A.DG17
 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG6,A.DG10,A.DG14,A.DG18
  step#1  pm(>>,forward)  area=8.38  rise=3.65 twist=33.7
  step#2  pm(>>,forward)  area=10.73 rise=3.26 twist=31.9
  strand#1 DNA glyco-bond=--- nts=3 GGG A.DG3,A.DG5,A.DG6
  strand#2 DNA glyco-bond=--- nts=3 GGG A.DG8,A.DG9,A.DG10
  strand#3 DNA glyco-bond=--- nts=3 GGG A.DG12,A.DG13,A.DG14
  strand#4 DNA glyco-bond=--- nts=3 GGG A.DG16,A.DG17,A.DG18

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2 stacking diagrams
 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG8,A.DG12,A.DG16
2 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG5,A.DG9,A.DG13,A.DG17
step#1 pm(>>,forward) area=8.38 rise=3.65 twist=33.7

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 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG5,A.DG9,A.DG13,A.DG17
3 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG6,A.DG10,A.DG14,A.DG18
step#2 pm(>>,forward) area=10.73 rise=3.26 twist=31.9

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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, UUUU, parallel, 3(-P-P-P), parallel(4+0)

 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG8,A.DG12,A.DG16
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG5,A.DG9,A.DG13,A.DG17
 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG6,A.DG10,A.DG14,A.DG18
  step#1  pm(>>,forward)  area=8.38  rise=3.65 twist=33.7
  step#2  pm(>>,forward)  area=10.73 rise=3.26 twist=31.9
  strand#1* U DNA glyco-bond=--- nts=3 GGG A.DG3,A.DG5,A.DG6 bulged-nts=1 T A.DT4
  strand#2  U DNA glyco-bond=--- nts=3 GGG A.DG8,A.DG9,A.DG10
  strand#3  U DNA glyco-bond=--- nts=3 GGG A.DG12,A.DG13,A.DG14
  strand#4  U DNA glyco-bond=--- nts=3 GGG A.DG16,A.DG17,A.DG18
  loop#1 type=propeller strands=[#1,#2] nts=1 T A.DT7
  loop#2 type=propeller strands=[#2,#3] nts=1 T A.DT11
  loop#3 type=propeller strands=[#3,#4] nts=1 T A.DT15

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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)