DSSR-curated G4 structure: PDB entry 2le6

Summary information

PDB id: 2le6
Class: DNA
Method: NMR
Summary: Structure of a dimeric all-parallel-stranded g-quadruplex stacked via the 5'-to-5' interface
Reference: Do NQ, Lim KW, Teo MH, Heddi B, Phan AT (2011): "Stacking of G-quadruplexes: NMR structure of a G-rich oligonucleotide with potential anti-HIV and anticancer activity." Nucleic Acids Res. doi: 10.1093/nar/gkr539.
Abstract: G-rich oligonucleotides T30695 (or T30923), with the sequence of (GGGT)(4), and T40214, with the sequence of (GGGC)(4), have been reported to exhibit anti-HIV and anticancer activity. Here we report on the structure of a dimeric G-quadruplex adopted by a derivative of these sequences in K(+) solution. It comprises two identical propeller-type parallel-stranded G-quadruplex subunits each containing three G-tetrad layers that are stacked via the 5'-5' interface. We demonstrated control over the stacking of the two monomeric subunits by sequence modifications. Our analysis of possible structures at the stacking interface provides a general principle for stacking of G-quadruplexes, which could have implications for the assembly and recognition of higher-order G-quadruplex structures.
G4 notes: 6 G-tetrads, 1 G4 helix, 2 G4 stems, 1 G4 coaxial stack, 3(-P-P-P), parallel(4+0), UUUU, coaxial interfaces: 5'/5'

Base-block schematics in six views

PyMOL session file	PDB file	View in 3Dmol.js

List of 6 G-tetrads

 1 glyco-bond=---- sugar=---- groove=---- planarity=0.130 type=planar nts=4 GGGG A.DG1,A.DG5,A.DG9,A.DG13
 2 glyco-bond=---- sugar=---- groove=---- planarity=0.118 type=planar nts=4 gGGG A.DI2,A.DG6,A.DG10,A.DG14
 3 glyco-bond=---- sugar=--.- groove=---- planarity=0.170 type=other  nts=4 GGGG A.DG3,A.DG7,A.DG11,A.DG15
 4 glyco-bond=---- sugar=---- groove=---- planarity=0.208 type=other  nts=4 GGGG B.DG1,B.DG5,B.DG9,B.DG13
 5 glyco-bond=---- sugar=---- groove=---- planarity=0.186 type=other  nts=4 gGGG B.DI2,B.DG6,B.DG10,B.DG14
 6 glyco-bond=---- sugar=--.- groove=---- planarity=0.170 type=other  nts=4 GGGG B.DG3,B.DG7,B.DG11,B.DG15

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, 6 G-tetrad layers, inter-molecular, with 2 stems

	1 glyco-bond=---- sugar=--.- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG7,A.DG11,A.DG15 2 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 gGGG A.DI2,A.DG6,A.DG10,A.DG14 3* glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG1,A.DG5,A.DG9,A.DG13 4 glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG B.DG9,B.DG5,B.DG1,B.DG13 5 glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGgG B.DG10,B.DG6,B.DI2,B.DG14 6 glyco-bond=---- sugar=.--- groove=---- Major-->WC nts=4 GGGG B.DG11,B.DG7,B.DG3,B.DG15 step#1 mp(<<,backward) area=10.23 rise=3.35 twist=29.4 step#2 mp(<<,backward) area=9.64 rise=3.36 twist=31.2 step#3 mm(<>,outward) area=30.24 rise=3.41 twist=-14.3 step#4 pm(>>,forward) area=10.72 rise=3.30 twist=30.9 step#5 pm(>>,forward) area=12.03 rise=3.35 twist=28.2 strand#1 DNA glyco-bond=------ sugar=-----. nts=6 GgGGGG A.DG3,A.DI2,A.DG1,B.DG9,B.DG10,B.DG11 strand#2 DNA glyco-bond=------ sugar=------ nts=6 GGGGGG A.DG7,A.DG6,A.DG5,B.DG5,B.DG6,B.DG7 strand#3 DNA glyco-bond=------ sugar=.----- nts=6 GGGGgG A.DG11,A.DG10,A.DG9,B.DG1,B.DI2,B.DG3 strand#4 DNA glyco-bond=------ sugar=------ nts=6 GGGGGG A.DG15,A.DG14,A.DG13,B.DG13,B.DG14,B.DG15 Download PDB file Interactive view in 3Dmol.js
5 stacking diagrams
	1 glyco-bond=---- sugar=--.- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG7,A.DG11,A.DG15 2 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 gGGG A.DI2,A.DG6,A.DG10,A.DG14 step#1 mp(<<,backward) area=10.23 rise=3.35 twist=29.4 Download PDB file Interactive view in 3Dmol.js
	2 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 gGGG A.DI2,A.DG6,A.DG10,A.DG14 3* glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG1,A.DG5,A.DG9,A.DG13 step#2 mp(<<,backward) area=9.64 rise=3.36 twist=31.2 Download PDB file Interactive view in 3Dmol.js
	3* glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG1,A.DG5,A.DG9,A.DG13 4 glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG B.DG9,B.DG5,B.DG1,B.DG13 step#3 mm(<>,outward) area=30.24 rise=3.41 twist=-14.3 Download PDB file Interactive view in 3Dmol.js
	4 glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG B.DG9,B.DG5,B.DG1,B.DG13 5 glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGgG B.DG10,B.DG6,B.DI2,B.DG14 step#4 pm(>>,forward) area=10.72 rise=3.30 twist=30.9 Download PDB file Interactive view in 3Dmol.js
	5 glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGgG B.DG10,B.DG6,B.DI2,B.DG14 6 glyco-bond=---- sugar=.--- groove=---- Major-->WC nts=4 GGGG B.DG11,B.DG7,B.DG3,B.DG15 step#5 pm(>>,forward) area=12.03 rise=3.35 twist=28.2 Download PDB file Interactive view in 3Dmol.js

List of 2 G4-stems

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, 3 loops, INTRA-molecular, UUUU, parallel, 3(-P-P-P), parallel(4+0)

 1  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG1,A.DG5,A.DG9,A.DG13
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 gGGG A.DI2,A.DG6,A.DG10,A.DG14
 3  glyco-bond=---- sugar=--.- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG7,A.DG11,A.DG15
  step#1  pm(>>,forward)  area=9.64  rise=3.36 twist=31.2
  step#2  pm(>>,forward)  area=10.23 rise=3.35 twist=29.4
  strand#1  U DNA glyco-bond=--- sugar=--- nts=3 GgG A.DG1,A.DI2,A.DG3
  strand#2  U DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG5,A.DG6,A.DG7
  strand#3  U DNA glyco-bond=--- sugar=--. nts=3 GGG A.DG9,A.DG10,A.DG11
  strand#4  U DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG13,A.DG14,A.DG15
  loop#1 type=propeller strands=[#1,#2] nts=1 T A.DT4
  loop#2 type=propeller strands=[#2,#3] nts=1 T A.DT8
  loop#3 type=propeller strands=[#3,#4] nts=1 T A.DT12

Download PDB file
Interactive view in 3Dmol.js

Stem#2, 3 G-tetrad layers, 3 loops, INTRA-molecular, UUUU, parallel, 3(-P-P-P), parallel(4+0)

 1  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG B.DG1,B.DG5,B.DG9,B.DG13
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 gGGG B.DI2,B.DG6,B.DG10,B.DG14
 3  glyco-bond=---- sugar=--.- groove=---- WC-->Major nts=4 GGGG B.DG3,B.DG7,B.DG11,B.DG15
  step#1  pm(>>,forward)  area=10.72 rise=3.30 twist=30.9
  step#2  pm(>>,forward)  area=12.03 rise=3.35 twist=28.2
  strand#1  U DNA glyco-bond=--- sugar=--- nts=3 GgG B.DG1,B.DI2,B.DG3
  strand#2  U DNA glyco-bond=--- sugar=--- nts=3 GGG B.DG5,B.DG6,B.DG7
  strand#3  U DNA glyco-bond=--- sugar=--. nts=3 GGG B.DG9,B.DG10,B.DG11
  strand#4  U DNA glyco-bond=--- sugar=--- nts=3 GGG B.DG13,B.DG14,B.DG15
  loop#1 type=propeller strands=[#1,#2] nts=1 T B.DT4
  loop#2 type=propeller strands=[#2,#3] nts=1 T B.DT8
  loop#3 type=propeller strands=[#3,#4] nts=1 T B.DT12