Summary information

PDB id
7cls
Class
DNA
Method
NMR
Summary
Solution structure of an intramolecular g-quadruplex containing a duplex bulge
Reference
Ngoc Nguyen TQ, Lim KW, Phan AT (2020): "Duplex formation in a G-quadruplex bulge." Nucleic Acids Res., 48, 10567-10575. doi: 10.1093/nar/gkaa738.
Abstract
Beyond the consensus definition of G-quadruplex-forming motifs with tracts of continuous guanines, G-quadruplexes harboring bulges in the G-tetrad core are prevalent in the human genome. Here, we study the incorporation of a duplex hairpin within a bulge of a G-quadruplex. The NMR solution structure of a G-quadruplex containing a duplex bulge was resolved, revealing the structural details of the junction between the duplex bulge and the G-quadruplex. Unexpectedly, instead of an orthogonal connection the duplex stem was observed to stack below the G-quadruplex forming a unique quadruplex-duplex junction. Breaking up of the immediate base pair step at the junction, coupled with a narrowing of the duplex groove within the context of the bulge, led to a progressive transition between the quadruplex and duplex segments. This study revealed that a duplex bulge can be formed at various positions of a G-quadruplex scaffold. In contrast to a non-structured bulge, the stability of a G-quadruplex slightly increases with an increase in the duplex bulge size. A G-quadruplex structure containing a duplex bulge of up to 33 nt in size was shown to form, which was much larger than the previously reported 7-nt bulge. With G-quadruplexes containing duplex bulges representing new structural motifs with potential biological significance, our findings would broaden the definition of potential G-quadruplex-forming sequences.
G4 notes
3 G-tetrads, 1 G4 helix, 1 G4 stem, 2(-P-P-P), parallel(4+0), UUUU

Base-block schematics in six views

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List of 3 G-tetrads

 1 glyco-bond=---- groove=---- planarity=0.124 type=planar nts=4 GGGG A.DG3,A.DG22,A.DG26,A.DG30
 2 glyco-bond=---- groove=---- planarity=0.204 type=other  nts=4 GGGG A.DG4,A.DG23,A.DG27,A.DG31
 3 glyco-bond=s--- groove=w--n planarity=0.060 type=planar nts=4 GGGG A.DG20,A.DG32,A.DG28,A.DG24

List of 1 G4-helix

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.DG22,A.DG26,A.DG30
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG23,A.DG27,A.DG31
 3  glyco-bond=s--- groove=n--w WC-->Major nts=4 GGGG A.DG20,A.DG24,A.DG28,A.DG32
  step#1  pm(>>,forward)  area=13.59 rise=3.50 twist=27.9
  step#2  pm(>>,forward)  area=10.60 rise=3.46 twist=31.7
  strand#1 DNA glyco-bond=--s nts=3 GGG A.DG3,A.DG4,A.DG20
  strand#2 DNA glyco-bond=--- nts=3 GGG A.DG22,A.DG23,A.DG24
  strand#3 DNA glyco-bond=--- nts=3 GGG A.DG26,A.DG27,A.DG28
  strand#4 DNA glyco-bond=--- nts=3 GGG A.DG30,A.DG31,A.DG32

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2 stacking diagrams
 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG22,A.DG26,A.DG30
2 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG23,A.DG27,A.DG31
step#1 pm(>>,forward) area=13.59 rise=3.50 twist=27.9

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 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG23,A.DG27,A.DG31
3 glyco-bond=s--- groove=n--w WC-->Major nts=4 GGGG A.DG20,A.DG24,A.DG28,A.DG32
step#2 pm(>>,forward) area=10.60 rise=3.46 twist=31.7

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List of 1 G4-stem

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.DG3,A.DG22,A.DG26,A.DG30
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG23,A.DG27,A.DG31
  step#1  pm(>>,forward)  area=13.59 rise=3.50 twist=27.9
  strand#1  U DNA glyco-bond=-- nts=2 GG A.DG3,A.DG4
  strand#2  U DNA glyco-bond=-- nts=2 GG A.DG22,A.DG23
  strand#3  U DNA glyco-bond=-- nts=2 GG A.DG26,A.DG27
  strand#4  U DNA glyco-bond=-- nts=2 GG A.DG30,A.DG31
  loop#1 type=propeller strands=[#1,#2] nts=17 ATCTGAGAATCAGATGT A.DA5,A.DT6,A.DC7,A.DT8,A.DG9,A.DA10,A.DG11,A.DA12,A.DA13,A.DT14,A.DC15,A.DA16,A.DG17,A.DA18,A.DT19,A.DG20,A.DT21
  loop#2 type=propeller strands=[#2,#3] nts=2 GT A.DG24,A.DT25
  loop#3 type=propeller strands=[#3,#4] nts=2 GT A.DG28,A.DT29

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List of 1 non-stem G4-loop (including the two closing Gs)

 1 type=V-shaped  helix=#1 nts=5 GTGGG A.DG20,A.DT21,A.DG22,A.DG23,A.DG24