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

PDB-id
2mb4
Class
DNA
Method
NMR
Summary
Solution structure of a stacked dimeric G-quadruplex formed by a segment of the human ceb1 minisatellite
Reference
Adrian, M., Ang, D.J., Lech, C.J., Heddi, B., Nicolas, A., Phan, A.T.: (2014) "Structure and Conformational Dynamics of a Stacked Dimeric G-Quadruplex Formed by the Human CEB1 Minisatellite." J.Am.Chem.Soc., 136, 6297-6305.
Abstract
CEB1 is a highly polymorphic human minisatellite. In yeast, the size variation of CEB1 tandem arrays has been associated with the capacity of the motif to form G-quadruplexes. Here we report on the NMR solution structure of a G-quadruplex formed by the CEB1 DNA G-rich fragment d(AGGGGGGAGGGAGGGTGG), harboring several G-tracts including one with six continuous guanines. This sequence forms a dimeric G-quadruplex involving the stacking of two subunits, each being a unique snapback parallel-stranded scaffold with three G-tetrad layers, three double-chain-reversal loops, and a V-shaped loop. The two subunits are stacked at their 5'-end tetrads, and multiple stacking rotamers may be present due to a high symmetry at the stacking interface. There is a conformational exchange in the millisecond time scale involving a swapping motion between two bases of the six-guanine tract. Our results not only add to the understanding of how the G-quadruplex formation in human minisatellite leads to genetic instability but also address the fundamental questions regarding stacking of G-quadruplexes and how a long continuous G-tract participates in the structure and conformational dynamics of G-quadruplexes.
G4 notes
6 G-tetrads, 1 G4 helix, 2 G4 stems, 1 G4 coaxial stack · 2(-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=s--- groove=w--n planarity=0.198 type=other  nts=4 GGGG A.DG3,A.DG15,A.DG11,A.DG7
 2 glyco-bond=---- groove=---- planarity=0.106 type=planar nts=4 GGGG A.DG5,A.DG9,A.DG13,A.DG17
 3 glyco-bond=---- groove=---- planarity=0.141 type=planar nts=4 GGGG A.DG6,A.DG10,A.DG14,A.DG18
 4 glyco-bond=s--- groove=w--n planarity=0.163 type=other  nts=4 GGGG B.DG3,B.DG15,B.DG11,B.DG7
 5 glyco-bond=---- groove=---- planarity=0.155 type=planar nts=4 GGGG B.DG5,B.DG9,B.DG13,B.DG17
 6 glyco-bond=---- groove=---- planarity=0.143 type=planar nts=4 GGGG B.DG6,B.DG10,B.DG14,B.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, 6 G-tetrad layers, inter-molecular, with 2 stems

 1  glyco-bond=s--- groove=w--n Major-->WC nts=4 GGGG A.DG3,A.DG15,A.DG11,A.DG7
 2  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG A.DG18,A.DG14,A.DG10,A.DG6
 3* glyco-bond=---- groove=---- Major-->WC nts=4 GGGG A.DG17,A.DG13,A.DG9,A.DG5
 4  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG B.DG9,B.DG13,B.DG17,B.DG5
 5  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG B.DG10,B.DG14,B.DG18,B.DG6
 6  glyco-bond=--s- groove=-wn- WC-->Major nts=4 GGGG B.DG11,B.DG15,B.DG3,B.DG7
  step#1  mp(<<,backward) area=11.51 rise=3.53 twist=30.0
  step#2  mp(<<,backward) area=9.04  rise=3.25 twist=31.4
  step#3  mm(<>,outward)  area=26.59 rise=3.55 twist=-8.7
  step#4  pm(>>,forward)  area=12.09 rise=3.38 twist=29.8
  step#5  pm(>>,forward)  area=9.65  rise=3.25 twist=31.3
  strand#1 DNA glyco-bond=s----- nts=6 GGGGGG A.DG3,A.DG18,A.DG17,B.DG9,B.DG10,B.DG11
  strand#2 DNA glyco-bond=------ nts=6 GGGGGG A.DG15,A.DG14,A.DG13,B.DG13,B.DG14,B.DG15
  strand#3 DNA glyco-bond=-----s nts=6 GGGGGG A.DG11,A.DG10,A.DG9,B.DG17,B.DG18,B.DG3
  strand#4 DNA glyco-bond=------ nts=6 GGGGGG A.DG7,A.DG6,A.DG5,B.DG5,B.DG6,B.DG7

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5 stacking diagrams
 1  glyco-bond=s--- groove=w--n Major-->WC nts=4 GGGG A.DG3,A.DG15,A.DG11,A.DG7
2 glyco-bond=---- groove=---- Major-->WC nts=4 GGGG A.DG18,A.DG14,A.DG10,A.DG6
step#1 mp(<<,backward) area=11.51 rise=3.53 twist=30.0

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 2  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG A.DG18,A.DG14,A.DG10,A.DG6
3* glyco-bond=---- groove=---- Major-->WC nts=4 GGGG A.DG17,A.DG13,A.DG9,A.DG5
step#2 mp(<<,backward) area=9.04 rise=3.25 twist=31.4

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 3* glyco-bond=---- groove=---- Major-->WC nts=4 GGGG A.DG17,A.DG13,A.DG9,A.DG5
4 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG B.DG9,B.DG13,B.DG17,B.DG5
step#3 mm(<>,outward) area=26.59 rise=3.55 twist=-8.7

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 4  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG B.DG9,B.DG13,B.DG17,B.DG5
5 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG B.DG10,B.DG14,B.DG18,B.DG6
step#4 pm(>>,forward) area=12.09 rise=3.38 twist=29.8

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 5  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG B.DG10,B.DG14,B.DG18,B.DG6
6 glyco-bond=--s- groove=-wn- WC-->Major nts=4 GGGG B.DG11,B.DG15,B.DG3,B.DG7
step#5 pm(>>,forward) area=9.65 rise=3.25 twist=31.3

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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, 2 G-tetrad layers, 3 loops, INTRA-molecular, UUUU, parallel, 2(-P-P-P), parallel(4+0)

 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG5,A.DG9,A.DG13,A.DG17
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG6,A.DG10,A.DG14,A.DG18
  step#1  pm(>>,forward)  area=9.04  rise=3.25 twist=31.4
  strand#1  U DNA glyco-bond=-- nts=2 GG A.DG5,A.DG6
  strand#2  U DNA glyco-bond=-- nts=2 GG A.DG9,A.DG10
  strand#3  U DNA glyco-bond=-- nts=2 GG A.DG13,A.DG14
  strand#4  U DNA glyco-bond=-- nts=2 GG A.DG17,A.DG18
  loop#1 type=propeller strands=[#1,#2] nts=2 GA A.DG7,A.DA8
  loop#2 type=propeller strands=[#2,#3] nts=2 GA A.DG11,A.DA12
  loop#3 type=propeller strands=[#3,#4] nts=2 GT A.DG15,A.DT16

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Stem#2, 2 G-tetrad layers, 3 loops, INTRA-molecular, UUUU, parallel, 2(-P-P-P), parallel(4+0)

 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG B.DG5,B.DG9,B.DG13,B.DG17
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG B.DG6,B.DG10,B.DG14,B.DG18
  step#1  pm(>>,forward)  area=12.09 rise=3.38 twist=29.8
  strand#1  U DNA glyco-bond=-- nts=2 GG B.DG5,B.DG6
  strand#2  U DNA glyco-bond=-- nts=2 GG B.DG9,B.DG10
  strand#3  U DNA glyco-bond=-- nts=2 GG B.DG13,B.DG14
  strand#4  U DNA glyco-bond=-- nts=2 GG B.DG17,B.DG18
  loop#1 type=propeller strands=[#1,#2] nts=2 GA B.DG7,B.DA8
  loop#2 type=propeller strands=[#2,#3] nts=2 GA B.DG11,B.DA12
  loop#3 type=propeller strands=[#3,#4] nts=2 GT B.DG15,B.DT16

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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 2 non-stem G4-loops (including the two closing Gs)

 1 type=V-shaped  helix=#1 nts=5 GGGGG A.DG3,A.DG4,A.DG5,A.DG6,A.DG7
 2 type=V-shaped  helix=#1 nts=5 GGGGG B.DG3,B.DG4,B.DG5,B.DG6,B.DG7