Summary information [schematics · tetrads · helices · stems · costacks · homepage]

PDB-id
6a85*
Class
DNA
Method
X-ray (1.45 Å)
Summary
Crystal structure of a novel DNA quadruplex
Reference
Liu, H.H., Wang, R., Yu, X., Shen, F.S., Lan, W.X., Haruehanroengra, P., Yao, Q.Q., Zhang, J., Chen, Y.Q., Li, S.H., Wu, B.X., Zheng, L.N., Ma, J.B., Lin, J.Z., Cao, C.Y., Li, J.X., Sheng, J., Gan, J.H.: (2018) "High-resolution DNA quadruplex structure containing all the A-, G-, C-, T-tetrads." Nucleic Acids Res., 46, 11627-11638.
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 [summary · tetrads · helices · stems · costacks · homepage]

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List of 8 G-tetrads [summary · schematics · helices · stems · costacks · homepage]

 1 glyco-bond=---- groove=---- planarity=0.208 type=other  nts=4 GGGG 1:A.DG2,1:B.DG2,2:A.DG2,2:B.DG2
 2 glyco-bond=---- groove=---- planarity=0.107 type=planar nts=4 GGGG 1:A.DG4,1:B.DG4,2:A.DG4,2:B.DG4
 3 glyco-bond=---- groove=---- planarity=0.300 type=bowl   nts=4 GGGG 1:A.DG6,1:B.DG6,2:A.DG6,2:B.DG6
 4 glyco-bond=---- groove=---- planarity=0.191 type=other  nts=4 GGGG 1:A.DG9,1:B.DG9,2:A.DG9,2:B.DG9
 5 glyco-bond=---- groove=---- planarity=0.219 type=bowl   nts=4 GGGG 1:A.DG10,1:B.DG10,2:A.DG10,2:B.DG10
 6 glyco-bond=---- groove=---- planarity=0.159 type=planar nts=4 GGGG 1:A.DG11,1:B.DG11,2:A.DG11,2:B.DG11
 7 glyco-bond=---- groove=---- planarity=0.091 type=planar nts=4 GGGG 1:A.DG13,1:B.DG13,2:A.DG13,2:B.DG13
 8 glyco-bond=---- 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 [summary · schematics · tetrads · stems · costacks · homepage]

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=---- groove=---- WC-->Major nts=4 GGGG 1:A.DG2,1:B.DG2,2:A.DG2,2:B.DG2
 2  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG 1:A.DG4,2:B.DG4,2:A.DG4,1:B.DG4
 3  glyco-bond=---- 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=--- nts=3 GGG 1:A.DG2,1:A.DG4,1:A.DG6
  strand#2 DNA glyco-bond=--- nts=3 GGG 1:B.DG2,2:B.DG4,2:B.DG6
  strand#3 DNA glyco-bond=--- nts=3 GGG 2:A.DG2,2:A.DG4,2:A.DG6
  strand#4 DNA glyco-bond=--- nts=3 GGG 2:B.DG2,1:B.DG4,1:B.DG6

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2 stacking diagrams
 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:A.DG2,1:B.DG2,2:A.DG2,2:B.DG2
2 glyco-bond=---- 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

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 2  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG 1:A.DG4,2:B.DG4,2:A.DG4,1:B.DG4
3 glyco-bond=---- 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

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

 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:A.DG9,1:B.DG9,2:A.DG9,2:B.DG9
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:A.DG10,1:B.DG10,2:A.DG10,2:B.DG10
 3  glyco-bond=---- 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=--- nts=3 GGG 1:A.DG9,1:A.DG10,1:A.DG11
  strand#2 DNA glyco-bond=--- nts=3 GGG 1:B.DG9,1:B.DG10,1:B.DG11
  strand#3 DNA glyco-bond=--- nts=3 GGG 2:A.DG9,2:A.DG10,2:A.DG11
  strand#4 DNA glyco-bond=--- nts=3 GGG 2:B.DG9,2:B.DG10,2:B.DG11

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2 stacking diagrams
 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:A.DG9,1:B.DG9,2:A.DG9,2:B.DG9
2 glyco-bond=---- 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

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 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:A.DG10,1:B.DG10,2:A.DG10,2:B.DG10
3 glyco-bond=---- 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

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List of 1 G4-stem [summary · schematics · tetrads · helices · costacks · homepage]

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=---- groove=---- WC-->Major nts=4 GGGG 1:A.DG9,1:B.DG9,2:A.DG9,2:B.DG9
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:A.DG10,1:B.DG10,2:A.DG10,2:B.DG10
 3  glyco-bond=---- 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=--- nts=3 GGG 1:A.DG9,1:A.DG10,1:A.DG11
  strand#2  U DNA glyco-bond=--- nts=3 GGG 1:B.DG9,1:B.DG10,1:B.DG11
  strand#3  U DNA glyco-bond=--- nts=3 GGG 2:A.DG9,2:A.DG10,2:A.DG11
  strand#4  U DNA glyco-bond=--- nts=3 GGG 2:B.DG9,2:B.DG10,2:B.DG11

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List of 0 G4 coaxial stacks [summary · schematics · tetrads · helices · stems · homepage]

List of 0 non-stem G4-loops (including the two closing Gs)