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

PDB-id
2lpw
Class
DNA
Method
NMR
Summary
Human ceb25 minisatellite G-quadruplex
Reference
Amrane, S., Adrian, M., Heddi, B., Serero, A., Nicolas, A., Mergny, J.L., Phan, A.T.: (2012) "Formation of Pearl-Necklace Monomorphic G-Quadruplexes in the Human CEB25 Minisatellite." J.Am.Chem.Soc., 134, 5807-5816.
Abstract
CEB25 is a human minisatellite locus, composed of slightly polymorphic 52-nucleotide (nt) tandem repeats. Genetically, most if not all individuals of the human population are heterozygous, carrying alleles ranging from 0.5 to 20 kb, maintained by mendelian inheritance but also subject to germline instability. To provide insights on the biological role of CEB25, we interrogated its structural features. We report the NMR structure of the G-quadruplex formed by the conserved 26-nt G-rich fragment of the CEB25 motif. In K(+) solution, this sequence forms a propeller-type parallel-stranded G-quadruplex involving a 9-nt central double-chain-reversal loop. This long loop is anchored to the 5'-end of the sequence by an A·T Watson-Crick base pair and a potential G·A noncanonical base pair. These base pairs contribute to the stability of the overall G-quadruplexstructure, as measured by an increase of about 17 kcal/mol in enthalpy or 6 °C in melting temperature. Further, we demonstrate that such a monomorphic structure is formed within longer sequence contexts folding into a pearl-necklace structure.
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]

PyMOL session file PDB file View in 3Dmol.js

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

 1 glyco-bond=---- groove=---- planarity=0.313 type=other  nts=4 GGGG A.DG3,A.DG7,A.DG19,A.DG23
 2 glyco-bond=---- groove=---- planarity=0.205 type=other  nts=4 GGGG A.DG4,A.DG8,A.DG20,A.DG24
 3 glyco-bond=---- groove=---- planarity=0.165 type=other  nts=4 GGGG A.DG5,A.DG9,A.DG21,A.DG25

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.DG7,A.DG19,A.DG23
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG8,A.DG20,A.DG24
 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG5,A.DG9,A.DG21,A.DG25
  step#1  pm(>>,forward)  area=17.51 rise=3.22 twist=21.9
  step#2  pm(>>,forward)  area=9.71  rise=3.45 twist=33.8
  strand#1 DNA glyco-bond=--- nts=3 GGG A.DG3,A.DG4,A.DG5
  strand#2 DNA glyco-bond=--- nts=3 GGG A.DG7,A.DG8,A.DG9
  strand#3 DNA glyco-bond=--- nts=3 GGG A.DG19,A.DG20,A.DG21
  strand#4 DNA glyco-bond=--- nts=3 GGG A.DG23,A.DG24,A.DG25

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2 stacking diagrams
 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG7,A.DG19,A.DG23
2 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG8,A.DG20,A.DG24
step#1 pm(>>,forward) area=17.51 rise=3.22 twist=21.9

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 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG8,A.DG20,A.DG24
3 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG5,A.DG9,A.DG21,A.DG25
step#2 pm(>>,forward) area=9.71 rise=3.45 twist=33.8

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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, 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.DG7,A.DG19,A.DG23
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG8,A.DG20,A.DG24
 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG5,A.DG9,A.DG21,A.DG25
  step#1  pm(>>,forward)  area=17.51 rise=3.22 twist=21.9
  step#2  pm(>>,forward)  area=9.71  rise=3.45 twist=33.8
  strand#1  U DNA glyco-bond=--- nts=3 GGG A.DG3,A.DG4,A.DG5
  strand#2  U DNA glyco-bond=--- nts=3 GGG A.DG7,A.DG8,A.DG9
  strand#3  U DNA glyco-bond=--- nts=3 GGG A.DG19,A.DG20,A.DG21
  strand#4  U DNA glyco-bond=--- nts=3 GGG A.DG23,A.DG24,A.DG25
  loop#1 type=propeller strands=[#1,#2] nts=1 T A.DT6
  loop#2 type=propeller strands=[#2,#3] nts=9 TGTAAGTGT A.DT10,A.DG11,A.DT12,A.DA13,A.DA14,A.DG15,A.DT16,A.DG17,A.DT18
  loop#3 type=propeller strands=[#3,#4] nts=1 T A.DT22

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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)