Summary information and primary citation

PDB-id
2kvy
Class
DNA
Method
NMR
Summary
NMR solution structure of the 4:1 complex between an uncharged distamycin a analogue and [d(tggggt)]4
Reference
Cosconati S, Marinelli L, Trotta R, Virno A, De Tito S, Romagnoli R, Pagano B, Limongelli V, Giancola C, Baraldi PG, Mayol L, Novellino E, Randazzo A (2010): "Structural and conformational requisites in DNA quadruplex groove binding: another piece to the puzzle." J.Am.Chem.Soc., 132, 6425-6433. doi: 10.1021/ja1003872.
Abstract
The study of DNA G-quadruplex stabilizers has enjoyed a great momentum in the late years due to their application as anticancer agents. The recognition of the grooves of these structural motifs is expected to result in a higher degree of selectivity over other DNA structures. Therefore, to achieve an enhanced knowledge on the structural and conformational requisites for quadruplex groove recognition, distamycin A, the only compound for which a pure groove binding has been proven, has been chemically modified. Surprisingly, structural and thermodynamic studies revealed that the absence of Coulombic interactions results in an unprecedented binding position in which both the groove and the 3' end of the DNA are occupied. This further contribution adds another piece to the so far elusive puzzle of the recognition between ligands and DNA quadruplexes and will serve as a platform for a rational design of new groove binders.
G4 notes
4 G-tetrads, 1 G4 helix, 1 G4 stem, UUUU, parallel, 4+0

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

PyMOL session file

Download PDB file

View in 3Dmol.js

List of 4 G-tetrads

 1 glyco-bond=---- sugar=-.-- groove=---- planarity=0.216 type=other  -- nts=4 GGGG A.DG2,D.DG20,B.DG8,C.DG14
 2 glyco-bond=---- sugar=-333 groove=---- planarity=0.226 type=other  -- nts=4 GGGG A.DG3,D.DG21,B.DG9,C.DG15
 3 glyco-bond=---- sugar=33-3 groove=---- planarity=0.379 type=other  -- nts=4 GGGG A.DG4,D.DG22,B.DG10,C.DG16
 4 glyco-bond=---- sugar=--.3 groove=---- planarity=0.855 type=bowl   -- nts=4 GGGG A.DG5,D.DG23,B.DG11,C.DG17

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=---- sugar=-.-- groove=---- WC-->Major -- nts=4 GGGG A.DG2,D.DG20,B.DG8,C.DG14
 2  glyco-bond=---- sugar=-333 groove=---- WC-->Major -- nts=4 GGGG A.DG3,D.DG21,B.DG9,C.DG15
 3  glyco-bond=---- sugar=33-3 groove=---- WC-->Major -- nts=4 GGGG A.DG4,D.DG22,B.DG10,C.DG16
 4  glyco-bond=---- sugar=--.3 groove=---- WC-->Major -- nts=4 GGGG A.DG5,D.DG23,B.DG11,C.DG17
  step#1  pm(>>,forward)  area=12.85 rise=3.41 twist=24.8
  step#2  pm(>>,forward)  area=16.42 rise=3.55 twist=22.8
  step#3  pm(>>,forward)  area=20.25 rise=4.02 twist=15.0
  strand#1 DNA glyco-bond=---- sugar=--3- nts=4 GGGG A.DG2,A.DG3,A.DG4,A.DG5
  strand#2 DNA glyco-bond=---- sugar=.33- nts=4 GGGG D.DG20,D.DG21,D.DG22,D.DG23
  strand#3 DNA glyco-bond=---- sugar=-3-. nts=4 GGGG B.DG8,B.DG9,B.DG10,B.DG11
  strand#4 DNA glyco-bond=---- sugar=-333 nts=4 GGGG C.DG14,C.DG15,C.DG16,C.DG17

Download PDB file
Interactive view in 3Dmol.js
3 stacking diagrams 
 1  glyco-bond=---- sugar=-.-- groove=---- WC-->Major -- nts=4 GGGG A.DG2,D.DG20,B.DG8,C.DG14
 2  glyco-bond=---- sugar=-333 groove=---- WC-->Major -- nts=4 GGGG A.DG3,D.DG21,B.DG9,C.DG15
  step#1  pm(>>,forward)  area=12.85 rise=3.41 twist=24.8

Download PDB file
Interactive view in 3Dmol.js

 
 2  glyco-bond=---- sugar=-333 groove=---- WC-->Major -- nts=4 GGGG A.DG3,D.DG21,B.DG9,C.DG15
 3  glyco-bond=---- sugar=33-3 groove=---- WC-->Major -- nts=4 GGGG A.DG4,D.DG22,B.DG10,C.DG16
  step#2  pm(>>,forward)  area=16.42 rise=3.55 twist=22.8

Download PDB file
Interactive view in 3Dmol.js

 
 3  glyco-bond=---- sugar=33-3 groove=---- WC-->Major -- nts=4 GGGG A.DG4,D.DG22,B.DG10,C.DG16
 4  glyco-bond=---- sugar=--.3 groove=---- WC-->Major -- nts=4 GGGG A.DG5,D.DG23,B.DG11,C.DG17
  step#3  pm(>>,forward)  area=20.25 rise=4.02 twist=15.0

Download PDB file
Interactive view in 3Dmol.js

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, 0 loops, inter-molecular, UUUU, parallel, 4+0
 1  glyco-bond=---- sugar=-.-- groove=---- WC-->Major -- nts=4 GGGG A.DG2,D.DG20,B.DG8,C.DG14
 2  glyco-bond=---- sugar=-333 groove=---- WC-->Major -- nts=4 GGGG A.DG3,D.DG21,B.DG9,C.DG15
 3  glyco-bond=---- sugar=33-3 groove=---- WC-->Major -- nts=4 GGGG A.DG4,D.DG22,B.DG10,C.DG16
 4  glyco-bond=---- sugar=--.3 groove=---- WC-->Major -- nts=4 GGGG A.DG5,D.DG23,B.DG11,C.DG17
  step#1  pm(>>,forward)  area=12.85 rise=3.41 twist=24.8
  step#2  pm(>>,forward)  area=16.42 rise=3.55 twist=22.8
  step#3  pm(>>,forward)  area=20.25 rise=4.02 twist=15.0
  strand#1  U DNA glyco-bond=---- sugar=--3- nts=4 GGGG A.DG2,A.DG3,A.DG4,A.DG5
  strand#2  U DNA glyco-bond=---- sugar=.33- nts=4 GGGG D.DG20,D.DG21,D.DG22,D.DG23
  strand#3  U DNA glyco-bond=---- sugar=-3-. nts=4 GGGG B.DG8,B.DG9,B.DG10,B.DG11
  strand#4  U DNA glyco-bond=---- sugar=-333 nts=4 GGGG C.DG14,C.DG15,C.DG16,C.DG17

Download PDB file
Interactive view in 3Dmol.js