Summary information and primary citation

PDB-id
2kaz
Class
DNA
Method
NMR
Summary
Folding topology of a bimolecular DNA quadruplex containing a stable mini-hairpin motif within the connecting loop
Reference
Balkwill GD, Garner TP, Williams HE, Searle MS (2009): "Folding topology of a bimolecular DNA quadruplex containing a stable mini-hairpin motif within the diagonal loop." J.Mol.Biol., 385, 1600-1615. doi: 10.1016/j.jmb.2008.11.050.
Abstract
We describe the NMR structural characterisation of a bimolecular anti-parallel DNA quadruplex d(G(3)ACGTAGTG(3))(2) containing an autonomously stable mini-hairpin motif inserted within the diagonal loop. A folding topology is identified that is different from that observed for the analogous d(G(3)T(4)G(3))(2) dimer with the two structures differing in the relative orientation of the diagonal loops. This appears to reflect specific base stacking interactions at the quadruplex-duplex interface that are not present in the structure with the T(4)-loop sequence. A truncated version of the bimolecular quadruplex d(G(2)ACGTAGTG(2))(2), with only two core G-tetrads, is less stable and forms a heterogeneous mixture of three 2-fold symmetric quadruplexes with different loop arrangements. We demonstrate that the nature of the loop sequence, its ability to form autonomously stable structure, the relative stabilities of the hairpin loop and core quadruplex, and the ability to form favourable stacking interactions between these two motifs are important factors in controlling DNA G-quadruplex topology.
G4 notes
3 G-tetrads, 1 G4 helix, 1 G4 stem, UUDD, anti-parallel:basket2, 2+2

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

PyMOL session file

Download PDB file

View in 3Dmol.js

List of 3 G-tetrads

 1 glyco-bond=ss-- sugar=---- groove=-w-n planarity=0.168 type=other  -- nts=4 GGGG A.DG1,B.DG24,A.DG13,B.DG16
 2 glyco-bond=--ss sugar=---- groove=-w-n planarity=0.271 type=other  -- nts=4 GGGG A.DG2,B.DG25,A.DG12,B.DG15
 3 glyco-bond=--ss sugar=---3 groove=-w-n planarity=0.279 type=bowl-2 -- nts=4 GGGG A.DG3,B.DG26,A.DG11,B.DG14

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, 3 G-tetrads, inter-molecular, with 1 stem
 1  glyco-bond=ss-- sugar=---- groove=-w-n Major-->WC -- nts=4 GGGG A.DG1,B.DG24,A.DG13,B.DG16
 2  glyco-bond=--ss sugar=---- groove=-w-n WC-->Major -- nts=4 GGGG A.DG2,B.DG25,A.DG12,B.DG15
 3  glyco-bond=--ss sugar=---3 groove=-w-n WC-->Major -- nts=4 GGGG A.DG3,B.DG26,A.DG11,B.DG14
  step#1  mm(<>,outward)  area=10.80 rise=3.50 twist=20.0
  step#2  pm(>>,forward)  area=13.31 rise=3.54 twist=27.6
  strand#1 DNA glyco-bond=s-- sugar=--- nts=3 GGG A.DG1,A.DG2,A.DG3
  strand#2 DNA glyco-bond=s-- sugar=--- nts=3 GGG B.DG24,B.DG25,B.DG26
  strand#3 DNA glyco-bond=-ss sugar=--- nts=3 GGG A.DG13,A.DG12,A.DG11
  strand#4 DNA glyco-bond=-ss sugar=--3 nts=3 GGG B.DG16,B.DG15,B.DG14

Download PDB file
Interactive view in 3Dmol.js
2 stacking diagrams 
 1  glyco-bond=ss-- sugar=---- groove=-w-n Major-->WC -- nts=4 GGGG A.DG1,B.DG24,A.DG13,B.DG16
 2  glyco-bond=--ss sugar=---- groove=-w-n WC-->Major -- nts=4 GGGG A.DG2,B.DG25,A.DG12,B.DG15
  step#1  mm(<>,outward)  area=10.80 rise=3.50 twist=20.0

Download PDB file
Interactive view in 3Dmol.js

 
 2  glyco-bond=--ss sugar=---- groove=-w-n WC-->Major -- nts=4 GGGG A.DG2,B.DG25,A.DG12,B.DG15
 3  glyco-bond=--ss sugar=---3 groove=-w-n WC-->Major -- nts=4 GGGG A.DG3,B.DG26,A.DG11,B.DG14
  step#2  pm(>>,forward)  area=13.31 rise=3.54 twist=27.6

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, 3 G-tetrads, 2 loops, inter-molecular, UUDD, anti-parallel:basket2, 2+2
 1  glyco-bond=ss-- sugar=---- groove=-w-n Major-->WC -- nts=4 GGGG A.DG1,B.DG24,A.DG13,B.DG16
 2  glyco-bond=--ss sugar=---- groove=-w-n WC-->Major -- nts=4 GGGG A.DG2,B.DG25,A.DG12,B.DG15
 3  glyco-bond=--ss sugar=---3 groove=-w-n WC-->Major -- nts=4 GGGG A.DG3,B.DG26,A.DG11,B.DG14
  step#1  mm(<>,outward)  area=10.80 rise=3.50 twist=20.0
  step#2  pm(>>,forward)  area=13.31 rise=3.54 twist=27.6
  strand#1  U DNA glyco-bond=s-- sugar=--- nts=3 GGG A.DG1,A.DG2,A.DG3
  strand#2  U DNA glyco-bond=s-- sugar=--- nts=3 GGG B.DG24,B.DG25,B.DG26
  strand#3  D DNA glyco-bond=-ss sugar=--- nts=3 GGG A.DG13,A.DG12,A.DG11
  strand#4  D DNA glyco-bond=-ss sugar=--3 nts=3 GGG B.DG16,B.DG15,B.DG14
  loop#1 type=diagonal  strands=[#1,#3] nts=7 ACGTAGT A.DA4,A.DC5,A.DG6,A.DT7,A.DA8,A.DG9,A.DT10
  loop#2 type=diagonal  strands=[#4,#2] nts=7 ACGTAGT B.DA17,B.DC18,B.DG19,B.DT20,B.DA21,B.DG22,B.DT23

Download PDB file
Interactive view in 3Dmol.js