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

PDB-id
2le6
Class
DNA
Method
NMR
Summary
Structure of a dimeric all-parallel-stranded G-quadruplex stacked via the 5'-to-5' interface
Reference
Do, N.Q., Lim, K.W., Teo, M.H., Heddi, B., Phan, A.T.: (2011) "Stacking of G-quadruplexes: NMR structure of a G-rich oligonucleotide with potential anti-HIV and anticancer activity." Nucleic Acids Res.
Abstract
G-rich oligonucleotides T30695 (or T30923), with the sequence of (GGGT)(4), and T40214, with the sequence of (GGGC)(4), have been reported to exhibit anti-HIV and anticancer activity. Here we report on the structure of a dimeric G-quadruplex adopted by a derivative of these sequences in K(+) solution. It comprises two identical propeller-type parallel-stranded G-quadruplex subunits each containing three G-tetrad layers that are stacked via the 5'-5' interface. We demonstrated control over the stacking of the two monomeric subunits by sequence modifications. Our analysis of possible structures at the stacking interface provides a general principle for stacking of G-quadruplexes, which could have implications for the assembly and recognition of higher-order G-quadruplex structures.
G4 notes
6 G-tetrads, 1 G4 helix, 2 G4 stems, 1 G4 coaxial stack · 3(-P-P-P), parallel(4+0), UUUU · coaxial interfaces: 5'/5'

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

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List of 6 G-tetrads [summary · schematics · helices · stems · costacks · homepage]

 1 glyco-bond=---- groove=---- planarity=0.130 type=planar nts=4 GGGG A.DG1,A.DG5,A.DG9,A.DG13
 2 glyco-bond=---- groove=---- planarity=0.118 type=planar nts=4 gGGG A.DI2,A.DG6,A.DG10,A.DG14
 3 glyco-bond=---- groove=---- planarity=0.170 type=other  nts=4 GGGG A.DG3,A.DG7,A.DG11,A.DG15
 4 glyco-bond=---- groove=---- planarity=0.208 type=other  nts=4 GGGG B.DG1,B.DG5,B.DG9,B.DG13
 5 glyco-bond=---- groove=---- planarity=0.186 type=other  nts=4 gGGG B.DI2,B.DG6,B.DG10,B.DG14
 6 glyco-bond=---- groove=---- planarity=0.170 type=other  nts=4 GGGG B.DG3,B.DG7,B.DG11,B.DG15

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, 6 G-tetrad layers, inter-molecular, with 2 stems

 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG7,A.DG11,A.DG15
 2  glyco-bond=---- groove=---- WC-->Major nts=4 gGGG A.DI2,A.DG6,A.DG10,A.DG14
 3* glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG1,A.DG5,A.DG9,A.DG13
 4  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG B.DG9,B.DG5,B.DG1,B.DG13
 5  glyco-bond=---- groove=---- Major-->WC nts=4 GGgG B.DG10,B.DG6,B.DI2,B.DG14
 6  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG B.DG11,B.DG7,B.DG3,B.DG15
  step#1  mp(<<,backward) area=10.23 rise=3.35 twist=29.4
  step#2  mp(<<,backward) area=9.64  rise=3.36 twist=31.2
  step#3  mm(<>,outward)  area=30.24 rise=3.41 twist=-14.3
  step#4  pm(>>,forward)  area=10.72 rise=3.30 twist=30.9
  step#5  pm(>>,forward)  area=12.03 rise=3.35 twist=28.2
  strand#1 DNA glyco-bond=------ nts=6 GgGGGG A.DG3,A.DI2,A.DG1,B.DG9,B.DG10,B.DG11
  strand#2 DNA glyco-bond=------ nts=6 GGGGGG A.DG7,A.DG6,A.DG5,B.DG5,B.DG6,B.DG7
  strand#3 DNA glyco-bond=------ nts=6 GGGGgG A.DG11,A.DG10,A.DG9,B.DG1,B.DI2,B.DG3
  strand#4 DNA glyco-bond=------ nts=6 GGGGGG A.DG15,A.DG14,A.DG13,B.DG13,B.DG14,B.DG15

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5 stacking diagrams
 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG7,A.DG11,A.DG15
2 glyco-bond=---- groove=---- WC-->Major nts=4 gGGG A.DI2,A.DG6,A.DG10,A.DG14
step#1 mp(<<,backward) area=10.23 rise=3.35 twist=29.4

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 2  glyco-bond=---- groove=---- WC-->Major nts=4 gGGG A.DI2,A.DG6,A.DG10,A.DG14
3* glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG1,A.DG5,A.DG9,A.DG13
step#2 mp(<<,backward) area=9.64 rise=3.36 twist=31.2

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 3* glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG1,A.DG5,A.DG9,A.DG13
4 glyco-bond=---- groove=---- Major-->WC nts=4 GGGG B.DG9,B.DG5,B.DG1,B.DG13
step#3 mm(<>,outward) area=30.24 rise=3.41 twist=-14.3

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 4  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG B.DG9,B.DG5,B.DG1,B.DG13
5 glyco-bond=---- groove=---- Major-->WC nts=4 GGgG B.DG10,B.DG6,B.DI2,B.DG14
step#4 pm(>>,forward) area=10.72 rise=3.30 twist=30.9

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 5  glyco-bond=---- groove=---- Major-->WC nts=4 GGgG B.DG10,B.DG6,B.DI2,B.DG14
6 glyco-bond=---- groove=---- Major-->WC nts=4 GGGG B.DG11,B.DG7,B.DG3,B.DG15
step#5 pm(>>,forward) area=12.03 rise=3.35 twist=28.2

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List of 2 G4-stems [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.DG1,A.DG5,A.DG9,A.DG13
 2  glyco-bond=---- groove=---- WC-->Major nts=4 gGGG A.DI2,A.DG6,A.DG10,A.DG14
 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG7,A.DG11,A.DG15
  step#1  pm(>>,forward)  area=9.64  rise=3.36 twist=31.2
  step#2  pm(>>,forward)  area=10.23 rise=3.35 twist=29.4
  strand#1  U DNA glyco-bond=--- nts=3 GgG A.DG1,A.DI2,A.DG3
  strand#2  U DNA glyco-bond=--- nts=3 GGG A.DG5,A.DG6,A.DG7
  strand#3  U DNA glyco-bond=--- nts=3 GGG A.DG9,A.DG10,A.DG11
  strand#4  U DNA glyco-bond=--- nts=3 GGG A.DG13,A.DG14,A.DG15
  loop#1 type=propeller strands=[#1,#2] nts=1 T A.DT4
  loop#2 type=propeller strands=[#2,#3] nts=1 T A.DT8
  loop#3 type=propeller strands=[#3,#4] nts=1 T A.DT12

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Stem#2, 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 B.DG1,B.DG5,B.DG9,B.DG13
 2  glyco-bond=---- groove=---- WC-->Major nts=4 gGGG B.DI2,B.DG6,B.DG10,B.DG14
 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG B.DG3,B.DG7,B.DG11,B.DG15
  step#1  pm(>>,forward)  area=10.72 rise=3.30 twist=30.9
  step#2  pm(>>,forward)  area=12.03 rise=3.35 twist=28.2
  strand#1  U DNA glyco-bond=--- nts=3 GgG B.DG1,B.DI2,B.DG3
  strand#2  U DNA glyco-bond=--- nts=3 GGG B.DG5,B.DG6,B.DG7
  strand#3  U DNA glyco-bond=--- nts=3 GGG B.DG9,B.DG10,B.DG11
  strand#4  U DNA glyco-bond=--- nts=3 GGG B.DG13,B.DG14,B.DG15
  loop#1 type=propeller strands=[#1,#2] nts=1 T B.DT4
  loop#2 type=propeller strands=[#2,#3] nts=1 T B.DT8
  loop#3 type=propeller strands=[#3,#4] nts=1 T B.DT12

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List of 1 G4 coaxial stack [summary · schematics · tetrads · helices · stems · homepage]

 1 G4 helix#1 contains 2 G4 stems: [#1,#2]  [5'/5']

List of 0 non-stem G4-loops (including the two closing Gs)