Summary information and primary citation

PDB-id
1qdi
Class
DNA
Method
NMR
Summary
The NMR study of DNA quadruplex structure, (12mer) DNA
Reference
Marathias VM, Wang KY, Kumar S, Pham TQ, Swaminathan S, Bolton PH (1996): "Determination of the number and location of the manganese binding sites of DNA quadruplexes in solution by EPR and NMR in the presence and absence of thrombin." J.Mol.Biol., 260, 378-394. doi: 10.1006/jmbi.1996.0408.
Abstract
The interaction of a DNA quadruplex with thrombin has been studied by first determining the sites of manganese binding to the quadruplex in the absence of thrombin. This has been followed by determining if the interactions with thrombin displace the bound manganese. A different DNA quadruplex has also been studied as a control. The refined solution structures of two DNA quadruplexes have been used to predict the electrostatic potentials of these DNAs. The calculated electrostatic potentials have been used to predict the locations of the binding sites of the paramagnetic ion manganese to these DNAs. The enhanced relaxation of DNA protons due to the binding of the paramagnetic metal ion Mn2+ has been used to experimentally determine the locations of the binding sites. The NMR results and the predictions based on the electrostatic potentials both place the binding sites of the manganese in the narrow grooves of these quadruplex DNAs. The predicted locations are spatially close to those experimentally observed, and the predicted and experimental locations also have similar electrostatic potential energy. These results have allowed a validation of the predictions of electrostatic potentials from structure. The 15mer quadruplex has two strong Mn2+ binding sites with one in each narrow groove. Both Mn2+ are released when the 15mer is complexed with thrombin, indicating that both narrow grooves are involved in the 15mer-thrombin interactions. The dimer quadruplex has a different structural motif than the 15mer and the presence of thrombin does not appreciably affect its interactions with Mn2+.
G4 notes
4 G-tetrads, 1 G4 helix, 1 G4 stem, UDDU, anti-parallel:basket, 2+2

Cartoon-block schematics in six views (download the tarball)

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List of 4 G-tetrads

 1 glyco-bond=s--s sugar=333- groove=w-n- planarity=0.474 type=bowl   -- nts=4 GGGG A.DG1,B.DG4,A.DG12,B.DG9
 2 glyco-bond=-ss- sugar=33-. groove=w-n- planarity=0.414 type=other  -- nts=4 GGGG A.DG2,B.DG3,A.DG11,B.DG10
 3 glyco-bond=s--s sugar=33-- groove=w-n- planarity=0.428 type=other  -- nts=4 GGGG A.DG3,B.DG2,A.DG10,B.DG11
 4 glyco-bond=-ss- sugar=33-3 groove=w-n- planarity=0.548 type=bowl   -- nts=4 GGGG A.DG4,B.DG1,A.DG9,B.DG12

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, 4 G-tetrads, inter-molecular, with 1 stem
 1  glyco-bond=s--s sugar=333- groove=w-n- Major-->WC -- nts=4 GGGG A.DG1,B.DG4,A.DG12,B.DG9
 2  glyco-bond=-ss- sugar=33-. groove=w-n- WC-->Major -- nts=4 GGGG A.DG2,B.DG3,A.DG11,B.DG10
 3  glyco-bond=s--s sugar=33-- groove=w-n- Major-->WC -- nts=4 GGGG A.DG3,B.DG2,A.DG10,B.DG11
 4  glyco-bond=-ss- sugar=33-3 groove=w-n- WC-->Major -- nts=4 GGGG A.DG4,B.DG1,A.DG9,B.DG12
  step#1  mm(<>,outward)  area=17.83 rise=3.38 twist=11.9
  step#2  pp(><,inward)   area=9.90  rise=3.24 twist=39.7
  step#3  mm(<>,outward)  area=13.52 rise=3.40 twist=21.8
  strand#1 DNA glyco-bond=s-s- sugar=3333 nts=4 GGGG A.DG1,A.DG2,A.DG3,A.DG4
  strand#2 DNA glyco-bond=-s-s sugar=3333 nts=4 GGGG B.DG4,B.DG3,B.DG2,B.DG1
  strand#3 DNA glyco-bond=-s-s sugar=3--- nts=4 GGGG A.DG12,A.DG11,A.DG10,A.DG9
  strand#4 DNA glyco-bond=s-s- sugar=-.-3 nts=4 GGGG B.DG9,B.DG10,B.DG11,B.DG12

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3 stacking diagrams 
 1  glyco-bond=s--s sugar=333- groove=w-n- Major-->WC -- nts=4 GGGG A.DG1,B.DG4,A.DG12,B.DG9
 2  glyco-bond=-ss- sugar=33-. groove=w-n- WC-->Major -- nts=4 GGGG A.DG2,B.DG3,A.DG11,B.DG10
  step#1  mm(<>,outward)  area=17.83 rise=3.38 twist=11.9

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 2  glyco-bond=-ss- sugar=33-. groove=w-n- WC-->Major -- nts=4 GGGG A.DG2,B.DG3,A.DG11,B.DG10
 3  glyco-bond=s--s sugar=33-- groove=w-n- Major-->WC -- nts=4 GGGG A.DG3,B.DG2,A.DG10,B.DG11
  step#2  pp(><,inward)   area=9.90  rise=3.24 twist=39.7

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 3  glyco-bond=s--s sugar=33-- groove=w-n- Major-->WC -- nts=4 GGGG A.DG3,B.DG2,A.DG10,B.DG11
 4  glyco-bond=-ss- sugar=33-3 groove=w-n- WC-->Major -- nts=4 GGGG A.DG4,B.DG1,A.DG9,B.DG12
  step#3  mm(<>,outward)  area=13.52 rise=3.40 twist=21.8

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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, 4 G-tetrads, 2 loops, inter-molecular, UDDU, anti-parallel:basket, 2+2
 1  glyco-bond=s--s sugar=333- groove=w-n- Major-->WC -- nts=4 GGGG A.DG1,B.DG4,A.DG12,B.DG9
 2  glyco-bond=-ss- sugar=33-. groove=w-n- WC-->Major -- nts=4 GGGG A.DG2,B.DG3,A.DG11,B.DG10
 3  glyco-bond=s--s sugar=33-- groove=w-n- Major-->WC -- nts=4 GGGG A.DG3,B.DG2,A.DG10,B.DG11
 4  glyco-bond=-ss- sugar=33-3 groove=w-n- WC-->Major -- nts=4 GGGG A.DG4,B.DG1,A.DG9,B.DG12
  step#1  mm(<>,outward)  area=17.83 rise=3.38 twist=11.9
  step#2  pp(><,inward)   area=9.90  rise=3.24 twist=39.7
  step#3  mm(<>,outward)  area=13.52 rise=3.40 twist=21.8
  strand#1  U DNA glyco-bond=s-s- sugar=3333 nts=4 GGGG A.DG1,A.DG2,A.DG3,A.DG4
  strand#2  D DNA glyco-bond=-s-s sugar=3333 nts=4 GGGG B.DG4,B.DG3,B.DG2,B.DG1
  strand#3  D DNA glyco-bond=-s-s sugar=3--- nts=4 GGGG A.DG12,A.DG11,A.DG10,A.DG9
  strand#4  U DNA glyco-bond=s-s- sugar=-.-3 nts=4 GGGG B.DG9,B.DG10,B.DG11,B.DG12
  loop#1 type=diagonal  strands=[#1,#3] nts=4 TTTT A.DT5,A.DT6,A.DT7,A.DT8
  loop#2 type=diagonal  strands=[#2,#4] nts=4 TTTT B.DT5,B.DT6,B.DT7,B.DT8

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