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

PDB-id
5ls8
Class
DNA
Method
X-ray (1.78 Å)
Summary
Light-activated ruthenium complex bound to a DNA quadruplex
Reference
McQuaid, K., Abell, H., Gurung, S.P., Allan, D.R., Winter, G., Sorensen, T., Cardin, D.J., Brazier, J.A., Cardin, C.J., Hall, J.P.: (2019) "Structural Studies Reveal Enantiospecific Recognition of a DNA G-Quadruplex by a Ruthenium Polypyridyl Complex." Angew.Chem.Int.Ed.Engl., 58, 9881-9885.
Abstract
By using X-ray crystallography, we show that the complexes Λ/Δ-[Ru(TAP)2 (11-CN-dppz)]2+ (TAP=1,4,5,8-tetraazaphenanthrene, dppz=dipyridophenazine) bind DNA G-quadruplex in an enantiospecific manner that parallels the specificity of these complexes with duplex DNA. The Λ complex crystallises with the normally parallel stranded d(TAGGGTTA) tetraplex to give the first such antiparallel strand assembly in which syn-guanosine is adjacent to the complex at the 5' end of the quadruplex core. SRCD measurements confirm that the same conformational switch occurs in solution. The Δ enantiomer, by contrast, is present in the structure but stacked at the ends of the assembly. In addition, we report the structure of Λ-[Ru(phen)2 (11-CN-dppz)]2+ bound to d(TCGGCGCCGA), a duplex-forming sequence, and use both structural models to provide insight into the motif-specific luminescence response of the isostructural phen analogue enantiomers.
G4 notes
3 G-tetrads, 1 G4 helix, 1 G4 stem · (2+2), UDUD

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=s-s- groove=wnwn planarity=0.456 type=bowl-2 nts=4 GGGG A.DG3,C.DG5,B.DG3,D.DG5
 2 glyco-bond=-s-s groove=wnwn planarity=0.358 type=other  nts=4 GGGG A.DG4,C.DG4,B.DG4,D.DG4
 3 glyco-bond=-s-s groove=wnwn planarity=0.500 type=bowl-2 nts=4 GGGG A.DG5,C.DG3,B.DG5,D.DG3

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, inter-molecular, with 1 stem

 1  glyco-bond=s-s- groove=wnwn Major-->WC nts=4 GGGG A.DG3,C.DG5,B.DG3,D.DG5
 2  glyco-bond=-s-s groove=wnwn WC-->Major nts=4 GGGG A.DG4,C.DG4,B.DG4,D.DG4
 3  glyco-bond=-s-s groove=wnwn WC-->Major nts=4 GGGG A.DG5,C.DG3,B.DG5,D.DG3
  step#1  mm(<>,outward)  area=12.59 rise=3.51 twist=18.8
  step#2  pm(>>,forward)  area=15.31 rise=3.55 twist=23.7
  strand#1 DNA glyco-bond=s-- nts=3 GGG A.DG3,A.DG4,A.DG5
  strand#2 DNA glyco-bond=-ss nts=3 GGG C.DG5,C.DG4,C.DG3
  strand#3 DNA glyco-bond=s-- nts=3 GGG B.DG3,B.DG4,B.DG5
  strand#4 DNA glyco-bond=-ss nts=3 GGG D.DG5,D.DG4,D.DG3

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2 stacking diagrams
 1  glyco-bond=s-s- groove=wnwn Major-->WC nts=4 GGGG A.DG3,C.DG5,B.DG3,D.DG5
2 glyco-bond=-s-s groove=wnwn WC-->Major nts=4 GGGG A.DG4,C.DG4,B.DG4,D.DG4
step#1 mm(<>,outward) area=12.59 rise=3.51 twist=18.8

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 2  glyco-bond=-s-s groove=wnwn WC-->Major nts=4 GGGG A.DG4,C.DG4,B.DG4,D.DG4
3 glyco-bond=-s-s groove=wnwn WC-->Major nts=4 GGGG A.DG5,C.DG3,B.DG5,D.DG3
step#2 pm(>>,forward) area=15.31 rise=3.55 twist=23.7

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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, 0 loops, inter-molecular, UDUD, anti-parallel, (2+2)

 1  glyco-bond=s-s- groove=wnwn Major-->WC nts=4 GGGG A.DG3,C.DG5,B.DG3,D.DG5
 2  glyco-bond=-s-s groove=wnwn WC-->Major nts=4 GGGG A.DG4,C.DG4,B.DG4,D.DG4
 3  glyco-bond=-s-s groove=wnwn WC-->Major nts=4 GGGG A.DG5,C.DG3,B.DG5,D.DG3
  step#1  mm(<>,outward)  area=12.59 rise=3.51 twist=18.8
  step#2  pm(>>,forward)  area=15.31 rise=3.55 twist=23.7
  strand#1  U DNA glyco-bond=s-- nts=3 GGG A.DG3,A.DG4,A.DG5
  strand#2  D DNA glyco-bond=-ss nts=3 GGG C.DG5,C.DG4,C.DG3
  strand#3  U DNA glyco-bond=s-- nts=3 GGG B.DG3,B.DG4,B.DG5
  strand#4  D DNA glyco-bond=-ss nts=3 GGG D.DG5,D.DG4,D.DG3

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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)