DSSR-enabled G4 identification/annotation

Summary information and primary citation

PDB-id: 6a85
Class: DNA
Method: X-ray (1.45 Å)
Summary: Crystal structure of a novel DNA quadruplex
Reference: Liu HH, Wang R, Yu X, Shen FS, Lan WX, Haruehanroengra P, Yao QQ, Zhang J, Chen YQ, Li SH, Wu BX, Zheng LN, Ma JB, Lin JZ, Cao CY, Li JX, Sheng J, Gan JH (2018): "High-resolution DNA quadruplex structure containing all the A-, G-, C-, T-tetrads." Nucleic Acids Res., 46, 11627-11638. doi: 10.1093/nar/gky902.
Abstract: DNA can form diverse structures, which predefine their physiological functions. Besides duplexes that carry the genetic information, quadruplexes are the most well-studied DNA structures. In addition to their important roles in recombination, replication, transcription and translation, DNA quadruplexes have also been applied as diagnostic aptamers and antidisease therapeutics. Herein we further expand the sequence and structure complexity of DNA quadruplex by presenting a high-resolution crystal structure of DNA1 (5'-AGAGAGATGGGTGCGTT-3'). This is the first quadruplex structure that contains all the internal A-, G-, C-, T-tetrads, A:T:A:T tetrads and bulged nucleotides in one single structure; as revealed by site-specific mutagenesis and biophysical studies, the central ATGGG motif plays important role in the quadruplex formation. Interestingly, our structure also provides great new insights into cation recognition, including the first-time reported Pb2+, by tetrad structures.
G4 notes: 8 G-tetrads, 2 G4 helices, 2 G4 stems, UUUU, parallel, 4+0

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

List of 8 G-tetrads

 1 glyco-bond=---- sugar=---- groove=---- planarity=0.208 type=other  -- nts=4 GGGG 1:A.DG2,1:B.DG2,2:A.DG2,2:B.DG2
 2 glyco-bond=---- sugar=---- groove=---- planarity=0.107 type=planar -- nts=4 GGGG 1:A.DG4,1:B.DG4,2:A.DG4,2:B.DG4
 3 glyco-bond=---- sugar=---- groove=---- planarity=0.300 type=bowl   -- nts=4 GGGG 1:A.DG6,1:B.DG6,2:A.DG6,2:B.DG6
 4 glyco-bond=---- sugar=---- groove=---- planarity=0.191 type=other  -- nts=4 GGGG 1:A.DG9,1:B.DG9,2:A.DG9,2:B.DG9
 5 glyco-bond=---- sugar=---- groove=---- planarity=0.219 type=bowl   -- nts=4 GGGG 1:A.DG10,1:B.DG10,2:A.DG10,2:B.DG10
 6 glyco-bond=---- sugar=---- groove=---- planarity=0.159 type=planar -- nts=4 GGGG 1:A.DG11,1:B.DG11,2:A.DG11,2:B.DG11
 7 glyco-bond=---- sugar=---- groove=---- planarity=0.091 type=planar -- nts=4 GGGG 1:A.DG13,1:B.DG13,2:A.DG13,2:B.DG13
 8 glyco-bond=---- sugar=---- groove=---- planarity=0.174 type=saddle -- nts=4 GGGG 1:A.DG15,1:B.DG15,2:A.DG15,2:B.DG15

List of 2 G4-helices

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=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:A.DG2,1:B.DG2,2:A.DG2,2:B.DG2 2 glyco-bond=---- sugar=---- groove=---- Major-->WC -- nts=4 GGGG 1:A.DG4,2:B.DG4,2:A.DG4,1:B.DG4 3 glyco-bond=---- sugar=---- groove=---- Major-->WC -- nts=4 GGGG 1:A.DG6,2:B.DG6,2:A.DG6,1:B.DG6 step#1 pm(>>,forward) area=0.00 rise=6.82 twist=146.0 step#2 pm(>>,forward) area=0.00 rise=6.89 twist=47.6 strand#1 DNA glyco-bond=--- sugar=--- nts=3 GGG 1:A.DG2,1:A.DG4,1:A.DG6 strand#2 DNA glyco-bond=--- sugar=--- nts=3 GGG 1:B.DG2,2:B.DG4,2:B.DG6 strand#3 DNA glyco-bond=--- sugar=--- nts=3 GGG 2:A.DG2,2:A.DG4,2:A.DG6 strand#4 DNA glyco-bond=--- sugar=--- nts=3 GGG 2:B.DG2,1:B.DG4,1:B.DG6 Download PDB file Interactive view in 3Dmol.js
2 stacking diagrams
	1 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:A.DG2,1:B.DG2,2:A.DG2,2:B.DG2 2 glyco-bond=---- sugar=---- groove=---- Major-->WC -- nts=4 GGGG 1:A.DG4,2:B.DG4,2:A.DG4,1:B.DG4 step#1 pm(>>,forward) area=0.00 rise=6.82 twist=146.0 Download PDB file Interactive view in 3Dmol.js
	2 glyco-bond=---- sugar=---- groove=---- Major-->WC -- nts=4 GGGG 1:A.DG4,2:B.DG4,2:A.DG4,1:B.DG4 3 glyco-bond=---- sugar=---- groove=---- Major-->WC -- nts=4 GGGG 1:A.DG6,2:B.DG6,2:A.DG6,1:B.DG6 step#2 pm(>>,forward) area=0.00 rise=6.89 twist=47.6 Download PDB file Interactive view in 3Dmol.js

Helix#2, 3 G-tetrads, inter-molecular, with 1 stem

	1 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:A.DG9,1:B.DG9,2:A.DG9,2:B.DG9 2 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:A.DG10,1:B.DG10,2:A.DG10,2:B.DG10 3 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:A.DG11,1:B.DG11,2:A.DG11,2:B.DG11 step#1 pm(>>,forward) area=12.93 rise=3.39 twist=24.7 step#2 pm(>>,forward) area=8.23 rise=3.34 twist=32.6 strand#1 DNA glyco-bond=--- sugar=--- nts=3 GGG 1:A.DG9,1:A.DG10,1:A.DG11 strand#2 DNA glyco-bond=--- sugar=--- nts=3 GGG 1:B.DG9,1:B.DG10,1:B.DG11 strand#3 DNA glyco-bond=--- sugar=--- nts=3 GGG 2:A.DG9,2:A.DG10,2:A.DG11 strand#4 DNA glyco-bond=--- sugar=--- nts=3 GGG 2:B.DG9,2:B.DG10,2:B.DG11 Download PDB file Interactive view in 3Dmol.js
2 stacking diagrams
	1 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:A.DG9,1:B.DG9,2:A.DG9,2:B.DG9 2 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:A.DG10,1:B.DG10,2:A.DG10,2:B.DG10 step#1 pm(>>,forward) area=12.93 rise=3.39 twist=24.7 Download PDB file Interactive view in 3Dmol.js
	2 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:A.DG10,1:B.DG10,2:A.DG10,2:B.DG10 3 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:A.DG11,1:B.DG11,2:A.DG11,2:B.DG11 step#2 pm(>>,forward) area=8.23 rise=3.34 twist=32.6 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, 0 loops, inter-molecular, UUUU, parallel, 4+0

 1  glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:A.DG4,1:B.DG4,2:A.DG4,2:B.DG4
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:A.DG6,1:B.DG6,2:A.DG6,2:B.DG6
  step#1  pm(>>,forward)  area=0.00  rise=6.89 twist=47.6
  strand#1* U DNA glyco-bond=-- sugar=-- nts=2 GG 1:A.DG4,1:A.DG6 bulged-nts=1 A 1:A.DA5
  strand#2* U DNA glyco-bond=-- sugar=-- nts=2 GG 1:B.DG4,1:B.DG6 bulged-nts=1 A 1:B.DA5
  strand#3* U DNA glyco-bond=-- sugar=-- nts=2 GG 2:A.DG4,2:A.DG6 bulged-nts=1 A 2:A.DA5
  strand#4* U DNA glyco-bond=-- sugar=-- nts=2 GG 2:B.DG4,2:B.DG6 bulged-nts=1 A 2:B.DA5

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Interactive view in 3Dmol.js

Stem#2, 3 G-tetrads, 0 loops, inter-molecular, UUUU, parallel, 4+0

 1  glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:A.DG9,1:B.DG9,2:A.DG9,2:B.DG9
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:A.DG10,1:B.DG10,2:A.DG10,2:B.DG10
 3  glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:A.DG11,1:B.DG11,2:A.DG11,2:B.DG11
  step#1  pm(>>,forward)  area=12.93 rise=3.39 twist=24.7
  step#2  pm(>>,forward)  area=8.23  rise=3.34 twist=32.6
  strand#1  U DNA glyco-bond=--- sugar=--- nts=3 GGG 1:A.DG9,1:A.DG10,1:A.DG11
  strand#2  U DNA glyco-bond=--- sugar=--- nts=3 GGG 1:B.DG9,1:B.DG10,1:B.DG11
  strand#3  U DNA glyco-bond=--- sugar=--- nts=3 GGG 2:A.DG9,2:A.DG10,2:A.DG11
  strand#4  U DNA glyco-bond=--- sugar=--- nts=3 GGG 2:B.DG9,2:B.DG10,2:B.DG11