DSSR-curated G4 structure: PDB entry 6a85

Summary information

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, 1 G4 stem, parallel(4+0), UUUU

Base-block schematics in six views

PyMOL session file	PDB file	View in 3Dmol.js

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-tetrad layers, inter-molecular

	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=-34.0 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=-34.0 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-tetrad layers, 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 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-tetrad layers, 0 loops, inter-molecular, UUUU, parallel, 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

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Detailed DSSR results for the G-quadruplex: PDB entry 6a85