DSSR-enabled G4 identification/annotation

Summary information and primary citation

PDB-id: 1oz8
Class: DNA
Method: NMR
Summary: Intramolecular higher-order packing of parallel quadruplexes comprising a g:g:g:g tetrad and a g(:a):g(:a):g(:a):g heptad of gga triplet repeat DNA
Reference: Matsugami A, Okuizumi T, Uesugi S, Katahira M (2003): "Intramolecular Higher Order Packing of Parallel Quadruplexes Comprising a G:G:G:G Tetrad and a G(:A):G(:A):G(:A):G Heptad of GGA Triplet Repeat DNA." J.BIOL.CHEM., 278, 28147-28153. doi: 10.1074/jbc.M303694200.
Abstract: GGA triplet repeats are widely dispersed throughout eukaryotic genomes and are frequently located within biologically important regions such as gene regulatory regions and recombination hot spot sites. We determined the structure of d(GGA)4 (12-mer) under physiological conditions and founded the formation of an intramolecular parallel quadruplex for the first time. Later, a similar architecture to that of the intramolecular parallel quadruplex was found for a telomere DNA in the crystalline state. Here, we have determined the structure of d(GGA)8 (24-mer) under physiological conditions. Two intramolecular parallel quadruplexes comprising a G:G:G:G tetrad and a G(:A):G(:A):G(:A):G heptad are formed in d(GGA)8. These quadruplexes are packed in a tail-to-tail manner. This is the first demonstration of the intramolecular higher order packing of quadruplexes at atomic resolution. K+ ions, but not Na+ ones, are critically required for the formation of this unique structure. The elucidated structure suggests the mechanisms underlying the biological events related to the GGA triplet repeat. Furthermore, in the light of the structure, the mode of the higher order packing of the telomere DNA is discussed.
G4 notes: 4 G-tetrads, 1 G4 helix, 2 G4 stems, 1 G4 coaxial stack, UUUU, parallel, 4+0, 2(-P-P-P), coaxial interfaces: 5'/5'

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

List of 4 G-tetrads

 1 glyco-bond=---- sugar=-... groove=---- planarity=0.322 type=other  O+ nts=4 GGGG A.DG1,A.DG4,A.DG7,A.DG10
 2 glyco-bond=---- sugar=-.-- groove=---- planarity=0.532 type=other  O+ nts=4 GGGG A.DG2,A.DG5,A.DG8,A.DG11
 3 glyco-bond=---- sugar=..-- groove=---- planarity=0.381 type=other  O+ nts=4 GGGG A.DG13,A.DG16,A.DG19,A.DG22
 4 glyco-bond=---- sugar=---. groove=---- planarity=0.522 type=bowl   O+ nts=4 GGGG A.DG14,A.DG17,A.DG20,A.DG23

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, INTRA-molecular, with 2 stems

	1 glyco-bond=---- sugar=-.-- groove=---- WC-->Major O+ nts=4 GGGG A.DG2,A.DG5,A.DG8,A.DG11 2* glyco-bond=---- sugar=-... groove=---- WC-->Major O+ nts=4 GGGG A.DG1,A.DG4,A.DG7,A.DG10 3 glyco-bond=---- sugar=..-- groove=---- WC-->Major O+ nts=4 GGGG A.DG13,A.DG16,A.DG19,A.DG22 4 glyco-bond=---- sugar=---. groove=---- WC-->Major O+ nts=4 GGGG A.DG14,A.DG17,A.DG20,A.DG23 step#1 mp(<<,backward) area=14.27 rise=3.26 twist=33.0 step#2 mm(<>,outward) area=26.12 rise=3.52 twist=-1.3 step#3 pm(>>,forward) area=9.52 rise=3.27 twist=30.8 strand#1 DNA glyco-bond=---- sugar=--.- nts=4 GGGG A.DG2,A.DG1,A.DG13,A.DG14 strand#2 DNA glyco-bond=---- sugar=...- nts=4 GGGG A.DG5,A.DG4,A.DG16,A.DG17 strand#3 DNA glyco-bond=---- sugar=-.-- nts=4 GGGG A.DG8,A.DG7,A.DG19,A.DG20 strand#4 DNA glyco-bond=---- sugar=-.-. nts=4 GGGG A.DG11,A.DG10,A.DG22,A.DG23 Download PDB file Interactive view in 3Dmol.js
3 stacking diagrams
	1 glyco-bond=---- sugar=-.-- groove=---- WC-->Major O+ nts=4 GGGG A.DG2,A.DG5,A.DG8,A.DG11 2* glyco-bond=---- sugar=-... groove=---- WC-->Major O+ nts=4 GGGG A.DG1,A.DG4,A.DG7,A.DG10 step#1 mp(<<,backward) area=14.27 rise=3.26 twist=33.0 Download PDB file Interactive view in 3Dmol.js
	2* glyco-bond=---- sugar=-... groove=---- WC-->Major O+ nts=4 GGGG A.DG1,A.DG4,A.DG7,A.DG10 3 glyco-bond=---- sugar=..-- groove=---- WC-->Major O+ nts=4 GGGG A.DG13,A.DG16,A.DG19,A.DG22 step#2 mm(<>,outward) area=26.12 rise=3.52 twist=-1.3 Download PDB file Interactive view in 3Dmol.js
	3 glyco-bond=---- sugar=..-- groove=---- WC-->Major O+ nts=4 GGGG A.DG13,A.DG16,A.DG19,A.DG22 4 glyco-bond=---- sugar=---. groove=---- WC-->Major O+ nts=4 GGGG A.DG14,A.DG17,A.DG20,A.DG23 step#3 pm(>>,forward) area=9.52 rise=3.27 twist=30.8 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, 2 G-tetrads, 3 loops, INTRA-molecular, UUUU, parallel, 4+0, 2(-P-P-P)

 1  glyco-bond=---- sugar=-... groove=---- WC-->Major O+ nts=4 GGGG A.DG1,A.DG4,A.DG7,A.DG10
 2  glyco-bond=---- sugar=-.-- groove=---- WC-->Major O+ nts=4 GGGG A.DG2,A.DG5,A.DG8,A.DG11
  step#1  pm(>>,forward)  area=14.27 rise=3.26 twist=33.0
  strand#1  U DNA glyco-bond=-- sugar=-- nts=2 GG A.DG1,A.DG2
  strand#2  U DNA glyco-bond=-- sugar=.. nts=2 GG A.DG4,A.DG5
  strand#3  U DNA glyco-bond=-- sugar=.- nts=2 GG A.DG7,A.DG8
  strand#4  U DNA glyco-bond=-- sugar=.- nts=2 GG A.DG10,A.DG11
  loop#1 type=propeller strands=[#1,#2] nts=1 A A.DA3
  loop#2 type=propeller strands=[#2,#3] nts=1 A A.DA6
  loop#3 type=propeller strands=[#3,#4] nts=1 A A.DA9

Download PDB file
Interactive view in 3Dmol.js

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

 1  glyco-bond=---- sugar=..-- groove=---- WC-->Major O+ nts=4 GGGG A.DG13,A.DG16,A.DG19,A.DG22
 2  glyco-bond=---- sugar=---. groove=---- WC-->Major O+ nts=4 GGGG A.DG14,A.DG17,A.DG20,A.DG23
  step#1  pm(>>,forward)  area=9.52  rise=3.27 twist=30.8
  strand#1  U DNA glyco-bond=-- sugar=.- nts=2 GG A.DG13,A.DG14
  strand#2  U DNA glyco-bond=-- sugar=.- nts=2 GG A.DG16,A.DG17
  strand#3  U DNA glyco-bond=-- sugar=-- nts=2 GG A.DG19,A.DG20
  strand#4  U DNA glyco-bond=-- sugar=-. nts=2 GG A.DG22,A.DG23
  loop#1 type=propeller strands=[#1,#2] nts=1 A A.DA15
  loop#2 type=propeller strands=[#2,#3] nts=1 A A.DA18
  loop#3 type=propeller strands=[#3,#4] nts=1 A A.DA21