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PDB-id
2jt7
Class
DNA
Method
NMR
Summary
NMR solution structure of the 4:1 distamycin a-[d(tggggt)]4 complex
Reference
Martino, L., Virno, A., Pagano, B., Virgilio, A., Di Micco, S., Galeone, A., Giancola, C., Bifulco, G., Mayol, L., Randazzo, A.: (2007) "Structural and thermodynamic studies of the interaction of distamycin A with the parallel quadruplex structure [d(TGGGGT)]4." J.Am.Chem.Soc., 129, 16048-16056.
Abstract
The complex between distamycin A and the parallel DNA quadruplex [d(TGGGGT)]4 has been studied by 1H NMR spectroscopy and isothermal titration calorimetry (ITC). To unambiguously assert that distamycin A interacts with the grooves of the quadruplex [d(TGGGGT)]4, we have analyzed the NMR titration profile of a modified quadruplex, namely [d(TGGMeGGT)]4, and we have applied the recently developed differential frequency-saturation transfer difference (DF-STD) method, for assessing the ligand-DNA binding mode. The three-dimensional structure of the 4:1 distamycin A/[d(TGGGGT)]4 complex has been determined by an in-depth NMR study followed by dynamics and mechanics calculations. All results unequivocally indicate that distamycin molecules interact with [d(TGGGGT)]4 in a 4:1 binding mode, with two antiparallel distamycin dimers that bind simultaneously two opposite grooves of the quadruplex. The affinity between distamycin A and [d(TGGGGT)]4 enhances ( approximately 10-fold) when the ratio of distamycin A to the quadruplex is increased. In this paper we report the first three-dimensional structure of a groove-binder molecule complexed to a DNA quadruplex structure.
G4 notes
4 G-tetrads, 1 G4 helix, 1 G4 stem · 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 4 G-tetrads [summary · schematics · helices · stems · costacks · homepage]

 1 glyco-bond=---- groove=---- planarity=0.223 type=other  nts=4 GGGG A.DG2,F.DG2,B.DG2,E.DG2
 2 glyco-bond=---- groove=---- planarity=0.430 type=other  nts=4 GGGG A.DG3,F.DG3,B.DG3,E.DG3
 3 glyco-bond=---- groove=---- planarity=0.313 type=saddle nts=4 GGGG A.DG4,F.DG4,B.DG4,E.DG4
 4 glyco-bond=---- groove=---- planarity=0.253 type=bowl-2 nts=4 GGGG A.DG5,F.DG5,B.DG5,E.DG5

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, 4 G-tetrad layers, inter-molecular, with 1 stem

 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG2,F.DG2,B.DG2,E.DG2
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG3,F.DG3,B.DG3,E.DG3
 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG4,F.DG4,B.DG4,E.DG4
 4  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG5,F.DG5,B.DG5,E.DG5
  step#1  pm(>>,forward)  area=19.05 rise=3.80 twist=18.8
  step#2  pm(>>,forward)  area=14.22 rise=3.72 twist=26.7
  step#3  pm(>>,forward)  area=14.85 rise=3.75 twist=25.3
  strand#1 DNA glyco-bond=---- nts=4 GGGG A.DG2,A.DG3,A.DG4,A.DG5
  strand#2 DNA glyco-bond=---- nts=4 GGGG F.DG2,F.DG3,F.DG4,F.DG5
  strand#3 DNA glyco-bond=---- nts=4 GGGG B.DG2,B.DG3,B.DG4,B.DG5
  strand#4 DNA glyco-bond=---- nts=4 GGGG E.DG2,E.DG3,E.DG4,E.DG5

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3 stacking diagrams
 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG2,F.DG2,B.DG2,E.DG2
2 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG3,F.DG3,B.DG3,E.DG3
step#1 pm(>>,forward) area=19.05 rise=3.80 twist=18.8

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 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG3,F.DG3,B.DG3,E.DG3
3 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG4,F.DG4,B.DG4,E.DG4
step#2 pm(>>,forward) area=14.22 rise=3.72 twist=26.7

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 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG4,F.DG4,B.DG4,E.DG4
4 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG5,F.DG5,B.DG5,E.DG5
step#3 pm(>>,forward) area=14.85 rise=3.75 twist=25.3

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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, 4 G-tetrad layers, 0 loops, inter-molecular, UUUU, parallel, parallel(4+0)

 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG2,F.DG2,B.DG2,E.DG2
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG3,F.DG3,B.DG3,E.DG3
 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG4,F.DG4,B.DG4,E.DG4
 4  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG5,F.DG5,B.DG5,E.DG5
  step#1  pm(>>,forward)  area=19.05 rise=3.80 twist=18.8
  step#2  pm(>>,forward)  area=14.22 rise=3.72 twist=26.7
  step#3  pm(>>,forward)  area=14.85 rise=3.75 twist=25.3
  strand#1  U DNA glyco-bond=---- nts=4 GGGG A.DG2,A.DG3,A.DG4,A.DG5
  strand#2  U DNA glyco-bond=---- nts=4 GGGG F.DG2,F.DG3,F.DG4,F.DG5
  strand#3  U DNA glyco-bond=---- nts=4 GGGG B.DG2,B.DG3,B.DG4,B.DG5
  strand#4  U DNA glyco-bond=---- nts=4 GGGG E.DG2,E.DG3,E.DG4,E.DG5

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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)