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

PDB-id
2mgn
Class
DNA
Method
NMR
Summary
Solution structure of a G-quadruplex bound to the bisquinolinium compound phen-dc3
Reference
Chung, W.J., Heddi, B., Hamon, F., Teulade-Fichou, M.P., Phan, A.T.: (2014) "Solution Structure of a G-quadruplex Bound to the Bisquinolinium Compound Phen-DC3." Angew.Chem.Int.Ed.Engl., 53, 999-1002.
Abstract
Phen-DC3 is a highly promising compound that specifically targets G-quadruplexes, with potent biological effects observed in vivo. We used NMR spectroscopy to solve the structure of the complex formed between Phen-DC3 and an intramolecular G-quadruplex derived from the c-myc promoter. Structural information revealed that Phen-DC3 interacts with the quadruplex through extensive π-stacking with guanine bases of the top G-tetrad. On the basis of our structure, modifications are proposed for the development of this compound for selective targeting of a specific G-quadruplex conformation.
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 [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=0.314 type=other  nts=4 GGGG A.DG4,A.DG8,A.DG13,A.DG17
 2 glyco-bond=---- groove=---- planarity=0.252 type=other  nts=4 GGGG A.DG5,A.DG9,A.DG14,A.DG18
 3 glyco-bond=-s-- groove=wn-- planarity=0.493 type=other  nts=4 GGGG A.DG6,A.DG24,A.DG15,A.DG19

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.DG4,A.DG8,A.DG13,A.DG17
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG5,A.DG9,A.DG14,A.DG18
 3  glyco-bond=-s-- groove=wn-- WC-->Major nts=4 GGGG A.DG6,A.DG24,A.DG15,A.DG19
  step#1  pm(>>,forward)  area=14.42 rise=3.16 twist=29.6
  step#2  pm(>>,forward)  area=11.55 rise=3.34 twist=30.9
  strand#1 DNA glyco-bond=--- nts=3 GGG A.DG4,A.DG5,A.DG6
  strand#2 DNA glyco-bond=--s nts=3 GGG A.DG8,A.DG9,A.DG24
  strand#3 DNA glyco-bond=--- nts=3 GGG A.DG13,A.DG14,A.DG15
  strand#4 DNA glyco-bond=--- nts=3 GGG A.DG17,A.DG18,A.DG19

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2 stacking diagrams
 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG8,A.DG13,A.DG17
2 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG5,A.DG9,A.DG14,A.DG18
step#1 pm(>>,forward) area=14.42 rise=3.16 twist=29.6

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 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG5,A.DG9,A.DG14,A.DG18
3 glyco-bond=-s-- groove=wn-- WC-->Major nts=4 GGGG A.DG6,A.DG24,A.DG15,A.DG19
step#2 pm(>>,forward) area=11.55 rise=3.34 twist=30.9

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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, 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.DG4,A.DG8,A.DG13,A.DG17
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG5,A.DG9,A.DG14,A.DG18
  step#1  pm(>>,forward)  area=14.42 rise=3.16 twist=29.6
  strand#1  U DNA glyco-bond=-- nts=2 GG A.DG4,A.DG5
  strand#2  U DNA glyco-bond=-- nts=2 GG A.DG8,A.DG9
  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 GT A.DG6,A.DT7
  loop#2 type=propeller strands=[#2,#3] nts=3 TGA A.DT10,A.DG11,A.DA12
  loop#3 type=propeller strands=[#3,#4] nts=2 GT A.DG15,A.DT16

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List of 0 G4 coaxial stacks [summary · schematics · tetrads · helices · stems · homepage]

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

 1 type=diagonal  helix=#1 nts=6 GGAAGG A.DG19,A.DG20,A.DA21,A.DA22,A.DG23,A.DG24