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

PDB-id
2hbn
Class
DNA
Method
X-ray (1.55 Å)
Summary
Crystallization of the tl+-form of the oxytricha nova G-quadruplex
Reference
Gill, M.L., Strobel, S.A., Loria, J.P.: (2006) "Crystallization and characterization of the thallium form of the Oxytricha nova G-quadruplex." Nucleic Acids Res., 34, 4506-4514.
Abstract
The crystal structure of the Tl+ form of the G-quadruplex formed from the Oxytricha nova telomere sequence, d(G4T4G4), has been solved to 1.55 A. This G-quadruplex contains five Tl+ ions, three of which are interspersed between adjacent G-quartet planes and one in each of the two thymine loops. The structure displays a high degree of similarity to the K+ crystal structure [Haider et al. (2002), J. Mol. Biol., 320, 189-200], including the number and location of the monovalent cation binding sites. The highly isomorphic nature of the two structures, which contain such a large number of monovalent binding sites (relative to nucleic acid content), verifies the ability of Tl+ to mimic K+ in nucleic acids. Information from this report confirms and extends the assignment of 205Tl resonances from a previous report [Gill et al. (2005), J. Am. Chem. Soc., 127, 16 723-16 732] where 205Tl NMR was used to study monovalent cation binding to this G-quadruplex. The assignment of these resonances provides evidence for the occurrence of conformational dynamics in the thymine loop region that is in slow exchange on the 205Tl timescale.
G4 notes
8 G-tetrads, 2 G4 helices, 2 G4 stems · (2+2), UDDU

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=s--s groove=w-n- planarity=0.205 type=other  nts=4 GGGG A.DG1,B.DG4,A.DG12,B.DG9
 2 glyco-bond=-ss- groove=w-n- planarity=0.157 type=planar nts=4 GGGG A.DG2,B.DG3,A.DG11,B.DG10
 3 glyco-bond=s--s groove=w-n- planarity=0.153 type=planar nts=4 GGGG A.DG3,B.DG2,A.DG10,B.DG11
 4 glyco-bond=-ss- groove=w-n- planarity=0.233 type=other  nts=4 GGGG A.DG4,B.DG1,A.DG9,B.DG12
 5 glyco-bond=s--s groove=w-n- planarity=0.240 type=other  nts=4 GGGG C.DG1,D.DG4,C.DG12,D.DG9
 6 glyco-bond=-ss- groove=w-n- planarity=0.170 type=other  nts=4 GGGG C.DG2,D.DG3,C.DG11,D.DG10
 7 glyco-bond=s--s groove=w-n- planarity=0.163 type=other  nts=4 GGGG C.DG3,D.DG2,C.DG10,D.DG11
 8 glyco-bond=-ss- groove=w-n- planarity=0.239 type=other  nts=4 GGGG C.DG4,D.DG1,C.DG9,D.DG12

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, 4 G-tetrad layers, inter-molecular, with 1 stem

 1  glyco-bond=s--s groove=w-n- Major-->WC nts=4 GGGG A.DG1,B.DG4,A.DG12,B.DG9
 2  glyco-bond=-ss- groove=w-n- WC-->Major nts=4 GGGG A.DG2,B.DG3,A.DG11,B.DG10
 3  glyco-bond=s--s groove=w-n- Major-->WC nts=4 GGGG A.DG3,B.DG2,A.DG10,B.DG11
 4  glyco-bond=-ss- groove=w-n- WC-->Major nts=4 GGGG A.DG4,B.DG1,A.DG9,B.DG12
  step#1  mm(<>,outward)  area=15.12 rise=3.45 twist=17.9
  step#2  pp(><,inward)   area=17.96 rise=3.55 twist=36.7
  step#3  mm(<>,outward)  area=15.75 rise=3.52 twist=16.9
  strand#1 DNA glyco-bond=s-s- nts=4 GGGG A.DG1,A.DG2,A.DG3,A.DG4
  strand#2 DNA glyco-bond=-s-s nts=4 GGGG B.DG4,B.DG3,B.DG2,B.DG1
  strand#3 DNA glyco-bond=-s-s nts=4 GGGG A.DG12,A.DG11,A.DG10,A.DG9
  strand#4 DNA glyco-bond=s-s- nts=4 GGGG B.DG9,B.DG10,B.DG11,B.DG12

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3 stacking diagrams
 1  glyco-bond=s--s groove=w-n- Major-->WC nts=4 GGGG A.DG1,B.DG4,A.DG12,B.DG9
2 glyco-bond=-ss- groove=w-n- WC-->Major nts=4 GGGG A.DG2,B.DG3,A.DG11,B.DG10
step#1 mm(<>,outward) area=15.12 rise=3.45 twist=17.9

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 2  glyco-bond=-ss- groove=w-n- WC-->Major nts=4 GGGG A.DG2,B.DG3,A.DG11,B.DG10
3 glyco-bond=s--s groove=w-n- Major-->WC nts=4 GGGG A.DG3,B.DG2,A.DG10,B.DG11
step#2 pp(><,inward) area=17.96 rise=3.55 twist=36.7

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 3  glyco-bond=s--s groove=w-n- Major-->WC nts=4 GGGG A.DG3,B.DG2,A.DG10,B.DG11
4 glyco-bond=-ss- groove=w-n- WC-->Major nts=4 GGGG A.DG4,B.DG1,A.DG9,B.DG12
step#3 mm(<>,outward) area=15.75 rise=3.52 twist=16.9

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Helix#2, 4 G-tetrad layers, inter-molecular, with 1 stem

 1  glyco-bond=s--s groove=w-n- Major-->WC nts=4 GGGG C.DG1,D.DG4,C.DG12,D.DG9
 2  glyco-bond=-ss- groove=w-n- WC-->Major nts=4 GGGG C.DG2,D.DG3,C.DG11,D.DG10
 3  glyco-bond=s--s groove=w-n- Major-->WC nts=4 GGGG C.DG3,D.DG2,C.DG10,D.DG11
 4  glyco-bond=-ss- groove=w-n- WC-->Major nts=4 GGGG C.DG4,D.DG1,C.DG9,D.DG12
  step#1  mm(<>,outward)  area=14.62 rise=3.53 twist=17.5
  step#2  pp(><,inward)   area=17.35 rise=3.53 twist=36.5
  step#3  mm(<>,outward)  area=14.63 rise=3.47 twist=18.1
  strand#1 DNA glyco-bond=s-s- nts=4 GGGG C.DG1,C.DG2,C.DG3,C.DG4
  strand#2 DNA glyco-bond=-s-s nts=4 GGGG D.DG4,D.DG3,D.DG2,D.DG1
  strand#3 DNA glyco-bond=-s-s nts=4 GGGG C.DG12,C.DG11,C.DG10,C.DG9
  strand#4 DNA glyco-bond=s-s- nts=4 GGGG D.DG9,D.DG10,D.DG11,D.DG12

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3 stacking diagrams
 1  glyco-bond=s--s groove=w-n- Major-->WC nts=4 GGGG C.DG1,D.DG4,C.DG12,D.DG9
2 glyco-bond=-ss- groove=w-n- WC-->Major nts=4 GGGG C.DG2,D.DG3,C.DG11,D.DG10
step#1 mm(<>,outward) area=14.62 rise=3.53 twist=17.5

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 2  glyco-bond=-ss- groove=w-n- WC-->Major nts=4 GGGG C.DG2,D.DG3,C.DG11,D.DG10
3 glyco-bond=s--s groove=w-n- Major-->WC nts=4 GGGG C.DG3,D.DG2,C.DG10,D.DG11
step#2 pp(><,inward) area=17.35 rise=3.53 twist=36.5

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 3  glyco-bond=s--s groove=w-n- Major-->WC nts=4 GGGG C.DG3,D.DG2,C.DG10,D.DG11
4 glyco-bond=-ss- groove=w-n- WC-->Major nts=4 GGGG C.DG4,D.DG1,C.DG9,D.DG12
step#3 mm(<>,outward) area=14.63 rise=3.47 twist=18.1

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List of 2 G4-stems [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, 4 G-tetrad layers, 2 loops, inter-molecular, UDDU, anti-parallel, (2+2)

 1  glyco-bond=s--s groove=w-n- Major-->WC nts=4 GGGG A.DG1,B.DG4,A.DG12,B.DG9
 2  glyco-bond=-ss- groove=w-n- WC-->Major nts=4 GGGG A.DG2,B.DG3,A.DG11,B.DG10
 3  glyco-bond=s--s groove=w-n- Major-->WC nts=4 GGGG A.DG3,B.DG2,A.DG10,B.DG11
 4  glyco-bond=-ss- groove=w-n- WC-->Major nts=4 GGGG A.DG4,B.DG1,A.DG9,B.DG12
  step#1  mm(<>,outward)  area=15.12 rise=3.45 twist=17.9
  step#2  pp(><,inward)   area=17.96 rise=3.55 twist=36.7
  step#3  mm(<>,outward)  area=15.75 rise=3.52 twist=16.9
  strand#1  U DNA glyco-bond=s-s- nts=4 GGGG A.DG1,A.DG2,A.DG3,A.DG4
  strand#2  D DNA glyco-bond=-s-s nts=4 GGGG B.DG4,B.DG3,B.DG2,B.DG1
  strand#3  D DNA glyco-bond=-s-s nts=4 GGGG A.DG12,A.DG11,A.DG10,A.DG9
  strand#4  U DNA glyco-bond=s-s- nts=4 GGGG B.DG9,B.DG10,B.DG11,B.DG12
  loop#1 type=diagonal  strands=[#1,#3] nts=4 TTTT A.DT5,A.DT6,A.DT7,A.DT8
  loop#2 type=diagonal  strands=[#2,#4] nts=4 TTTT B.DT5,B.DT6,B.DT7,B.DT8

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Stem#2, 4 G-tetrad layers, 2 loops, inter-molecular, UDDU, anti-parallel, (2+2)

 1  glyco-bond=s--s groove=w-n- Major-->WC nts=4 GGGG C.DG1,D.DG4,C.DG12,D.DG9
 2  glyco-bond=-ss- groove=w-n- WC-->Major nts=4 GGGG C.DG2,D.DG3,C.DG11,D.DG10
 3  glyco-bond=s--s groove=w-n- Major-->WC nts=4 GGGG C.DG3,D.DG2,C.DG10,D.DG11
 4  glyco-bond=-ss- groove=w-n- WC-->Major nts=4 GGGG C.DG4,D.DG1,C.DG9,D.DG12
  step#1  mm(<>,outward)  area=14.62 rise=3.53 twist=17.5
  step#2  pp(><,inward)   area=17.35 rise=3.53 twist=36.5
  step#3  mm(<>,outward)  area=14.63 rise=3.47 twist=18.1
  strand#1  U DNA glyco-bond=s-s- nts=4 GGGG C.DG1,C.DG2,C.DG3,C.DG4
  strand#2  D DNA glyco-bond=-s-s nts=4 GGGG D.DG4,D.DG3,D.DG2,D.DG1
  strand#3  D DNA glyco-bond=-s-s nts=4 GGGG C.DG12,C.DG11,C.DG10,C.DG9
  strand#4  U DNA glyco-bond=s-s- nts=4 GGGG D.DG9,D.DG10,D.DG11,D.DG12
  loop#1 type=diagonal  strands=[#1,#3] nts=4 TTTT C.DT5,C.DT6,C.DT7,C.DT8
  loop#2 type=diagonal  strands=[#2,#4] nts=4 TTTT D.DT5,D.DT6,D.DT7,D.DT8

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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)