DSSR-enabled G4 identification/annotation

Summary information and primary citation

PDB-id: 4r44
Class: DNA
Method: X-ray (2.695 Å)
Summary: Racemic crystal structure of a tetramolecular DNA g-quadruplex
Reference: Mandal PK, Collie GW, Kauffmann B, Huc I (2014): "Racemic DNA crystallography." Angew.Chem.Int.Ed.Engl., 53, 14424-14427. doi: 10.1002/anie.201409014.
Abstract: Racemates increase the chances of crystallization by allowing molecular contacts to be formed in a greater number of ways. With the advent of protein synthesis, the production of protein racemates and racemic-protein crystallography are now possible. Curiously, racemic DNA crystallography had not been investigated despite the commercial availability of L- and D-deoxyribo-oligonucleotides. Here, we report a study into racemic DNA crystallography showing the strong propensity of racemic DNA mixtures to form racemic crystals. We describe racemic crystal structures of various DNA sequences and folded conformations, including duplexes, quadruplexes, and a four-way junction, showing that the advantages of racemic crystallography should extend to DNA.
G4 notes: 8 G-tetrads, 1 G4 helix, 2 G4 stems, 1 G4 coaxial stack, UUUU, parallel, 4+0, coaxial interfaces: 5'/5'

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

List of 8 G-tetrads

 1 glyco-bond=---- sugar=--.- groove=---- planarity=0.248 type=bowl   -- nts=4 GGGG 1:A.DG2,1:D.DG32,1:C.DG22,1:B.DG12
 2 glyco-bond=---- sugar=---- groove=---- planarity=0.210 type=bowl   -- nts=4 GGGG 1:A.DG3,1:D.DG33,1:C.DG23,1:B.DG13
 3 glyco-bond=---- sugar=---- groove=---- planarity=0.139 type=planar -- nts=4 GGGG 1:A.DG4,1:D.DG34,1:C.DG24,1:B.DG14
 4 glyco-bond=---- sugar=---- groove=---- planarity=0.198 type=bowl   -- nts=4 GGGG 1:A.DG5,1:D.DG35,1:C.DG25,1:B.DG15
 5 glyco-bond=---- sugar=3333 groove=---- planarity=0.081 type=planar -- nts=4 GGGG 1:E.DG42,1:H.DG72,1:G.DG62,1:F.DG52
 6 glyco-bond=---- sugar=---- groove=---- planarity=0.293 type=bowl   -- nts=4 GGGG 1:E.DG43,1:H.DG73,1:G.DG63,1:F.DG53
 7 glyco-bond=---- sugar=---- groove=---- planarity=0.201 type=bowl   -- nts=4 GGGG 1:E.DG44,1:H.DG74,1:G.DG64,1:F.DG54
 8 glyco-bond=---- sugar=---- groove=---- planarity=0.243 type=bowl   -- nts=4 GGGG 1:E.DG45,1:H.DG75,1:G.DG65,1:F.DG55

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, 8 G-tetrads, inter-molecular, with 2 stems

	1 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:A.DG5,1:D.DG35,1:C.DG25,1:B.DG15 2 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:A.DG4,1:D.DG34,1:C.DG24,1:B.DG14 3 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:A.DG3,1:D.DG33,1:C.DG23,1:B.DG13 4* glyco-bond=---- sugar=--.- groove=---- WC-->Major -- nts=4 GGGG 1:A.DG2,1:D.DG32,1:C.DG22,1:B.DG12 5 glyco-bond=---- sugar=3333 groove=---- Major-->WC -- nts=4 GGGG 1:F.DG52,1:G.DG62,1:H.DG72,1:E.DG42 6 glyco-bond=---- sugar=---- groove=---- Major-->WC -- nts=4 GGGG 1:F.DG53,1:G.DG63,1:H.DG73,1:E.DG43 7 glyco-bond=---- sugar=---- groove=---- Major-->WC -- nts=4 GGGG 1:F.DG54,1:G.DG64,1:H.DG74,1:E.DG44 8 glyco-bond=---- sugar=---- groove=---- Major-->WC -- nts=4 GGGG 1:F.DG55,1:G.DG65,1:H.DG75,1:E.DG45 step#1 mp(<<,backward) area=12.14 rise=3.40 twist=28.2 step#2 mp(<<,backward) area=10.01 rise=3.34 twist=31.6 step#3 mp(<<,backward) area=10.79 rise=3.46 twist=28.4 step#4 mm(<>,outward) area=14.69 rise=3.70 twist=16.9 step#5 pm(>>,forward) area=8.95 rise=3.61 twist=29.5 step#6 pm(>>,forward) area=7.96 rise=3.42 twist=33.2 step#7 pm(>>,forward) area=11.99 rise=3.48 twist=26.2 strand#1 DNA glyco-bond=-------- sugar=----3--- nts=8 GGGGGGGG 1:A.DG5,1:A.DG4,1:A.DG3,1:A.DG2,1:F.DG52,1:F.DG53,1:F.DG54,1:F.DG55 strand#2 DNA glyco-bond=-------- sugar=----3--- nts=8 GGGGGGGG 1:D.DG35,1:D.DG34,1:D.DG33,1:D.DG32,1:G.DG62,1:G.DG63,1:G.DG64,1:G.DG65 strand#3 DNA glyco-bond=-------- sugar=---.3--- nts=8 GGGGGGGG 1:C.DG25,1:C.DG24,1:C.DG23,1:C.DG22,1:H.DG72,1:H.DG73,1:H.DG74,1:H.DG75 strand#4 DNA glyco-bond=-------- sugar=----3--- nts=8 GGGGGGGG 1:B.DG15,1:B.DG14,1:B.DG13,1:B.DG12,1:E.DG42,1:E.DG43,1:E.DG44,1:E.DG45 Download PDB file Interactive view in 3Dmol.js
7 stacking diagrams
	1 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:A.DG5,1:D.DG35,1:C.DG25,1:B.DG15 2 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:A.DG4,1:D.DG34,1:C.DG24,1:B.DG14 step#1 mp(<<,backward) area=12.14 rise=3.40 twist=28.2 Download PDB file Interactive view in 3Dmol.js
	2 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:A.DG4,1:D.DG34,1:C.DG24,1:B.DG14 3 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:A.DG3,1:D.DG33,1:C.DG23,1:B.DG13 step#2 mp(<<,backward) area=10.01 rise=3.34 twist=31.6 Download PDB file Interactive view in 3Dmol.js
	3 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:A.DG3,1:D.DG33,1:C.DG23,1:B.DG13 4* glyco-bond=---- sugar=--.- groove=---- WC-->Major -- nts=4 GGGG 1:A.DG2,1:D.DG32,1:C.DG22,1:B.DG12 step#3 mp(<<,backward) area=10.79 rise=3.46 twist=28.4 Download PDB file Interactive view in 3Dmol.js
	4* glyco-bond=---- sugar=--.- groove=---- WC-->Major -- nts=4 GGGG 1:A.DG2,1:D.DG32,1:C.DG22,1:B.DG12 5 glyco-bond=---- sugar=3333 groove=---- Major-->WC -- nts=4 GGGG 1:F.DG52,1:G.DG62,1:H.DG72,1:E.DG42 step#4 mm(<>,outward) area=14.69 rise=3.70 twist=16.9 Download PDB file Interactive view in 3Dmol.js
	5 glyco-bond=---- sugar=3333 groove=---- Major-->WC -- nts=4 GGGG 1:F.DG52,1:G.DG62,1:H.DG72,1:E.DG42 6 glyco-bond=---- sugar=---- groove=---- Major-->WC -- nts=4 GGGG 1:F.DG53,1:G.DG63,1:H.DG73,1:E.DG43 step#5 pm(>>,forward) area=8.95 rise=3.61 twist=29.5 Download PDB file Interactive view in 3Dmol.js
	6 glyco-bond=---- sugar=---- groove=---- Major-->WC -- nts=4 GGGG 1:F.DG53,1:G.DG63,1:H.DG73,1:E.DG43 7 glyco-bond=---- sugar=---- groove=---- Major-->WC -- nts=4 GGGG 1:F.DG54,1:G.DG64,1:H.DG74,1:E.DG44 step#6 pm(>>,forward) area=7.96 rise=3.42 twist=33.2 Download PDB file Interactive view in 3Dmol.js
	7 glyco-bond=---- sugar=---- groove=---- Major-->WC -- nts=4 GGGG 1:F.DG54,1:G.DG64,1:H.DG74,1:E.DG44 8 glyco-bond=---- sugar=---- groove=---- Major-->WC -- nts=4 GGGG 1:F.DG55,1:G.DG65,1:H.DG75,1:E.DG45 step#7 pm(>>,forward) area=11.99 rise=3.48 twist=26.2 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, 4 G-tetrads, 0 loops, inter-molecular, UUUU, parallel, 4+0

 1  glyco-bond=---- sugar=--.- groove=---- WC-->Major -- nts=4 GGGG 1:A.DG2,1:D.DG32,1:C.DG22,1:B.DG12
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:A.DG3,1:D.DG33,1:C.DG23,1:B.DG13
 3  glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:A.DG4,1:D.DG34,1:C.DG24,1:B.DG14
 4  glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:A.DG5,1:D.DG35,1:C.DG25,1:B.DG15
  step#1  pm(>>,forward)  area=10.79 rise=3.46 twist=28.4
  step#2  pm(>>,forward)  area=10.01 rise=3.34 twist=31.6
  step#3  pm(>>,forward)  area=12.14 rise=3.40 twist=28.2
  strand#1  U DNA glyco-bond=---- sugar=---- nts=4 GGGG 1:A.DG2,1:A.DG3,1:A.DG4,1:A.DG5
  strand#2  U DNA glyco-bond=---- sugar=---- nts=4 GGGG 1:D.DG32,1:D.DG33,1:D.DG34,1:D.DG35
  strand#3  U DNA glyco-bond=---- sugar=.--- nts=4 GGGG 1:C.DG22,1:C.DG23,1:C.DG24,1:C.DG25
  strand#4  U DNA glyco-bond=---- sugar=---- nts=4 GGGG 1:B.DG12,1:B.DG13,1:B.DG14,1:B.DG15

Download PDB file
Interactive view in 3Dmol.js

Stem#2, 4 G-tetrads, 0 loops, inter-molecular, UUUU, parallel, 4+0

 1  glyco-bond=---- sugar=3333 groove=---- WC-->Major -- nts=4 GGGG 1:E.DG42,1:H.DG72,1:G.DG62,1:F.DG52
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:E.DG43,1:H.DG73,1:G.DG63,1:F.DG53
 3  glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:E.DG44,1:H.DG74,1:G.DG64,1:F.DG54
 4  glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:E.DG45,1:H.DG75,1:G.DG65,1:F.DG55
  step#1  pm(>>,forward)  area=8.95  rise=3.61 twist=29.5
  step#2  pm(>>,forward)  area=7.96  rise=3.42 twist=33.2
  step#3  pm(>>,forward)  area=11.99 rise=3.48 twist=26.2
  strand#1  U DNA glyco-bond=---- sugar=3--- nts=4 GGGG 1:E.DG42,1:E.DG43,1:E.DG44,1:E.DG45
  strand#2  U DNA glyco-bond=---- sugar=3--- nts=4 GGGG 1:H.DG72,1:H.DG73,1:H.DG74,1:H.DG75
  strand#3  U DNA glyco-bond=---- sugar=3--- nts=4 GGGG 1:G.DG62,1:G.DG63,1:G.DG64,1:G.DG65
  strand#4  U DNA glyco-bond=---- sugar=3--- nts=4 GGGG 1:F.DG52,1:F.DG53,1:F.DG54,1:F.DG55