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PDB-id
2akg
Class
DNA
Method
NMR
Summary
Thallium form of the G-quadruplex from oxytricha nova, d(g4t4g4)2
Reference
Gill, M.L., Strobel, S.A., Loria, J.P.: (2005) "(205)Tl NMR methods for the characterization of monovalent cation binding to nucleic acids." J.Am.Chem.Soc., 127, 16723-16732.
Abstract
Monovalent cations play an important role in many biological functions. The guanine rich sequence, d(G4T4G4), requires monovalent cations for formation of the G-quadruplex, d(G4T4G4)2. This requirement can be satisfied by thallium (Tl+), a potassium (K+) surrogate. To verify that the structure of d(G4T4G4)2 in the presence of Tl+ is similar to the K+-form of the G-quadruplex, the solution structure of the Tl+-form of d(G4T4G4)2 was determined. The 10 lowest energy structures have an all atom RMSD of 0.76 +/- 0.16 A. Comparison of this structure to the identical G-quadruplex formed in the presence of K+ validates the isomorphous nature of Tl+ and K+. Using a 1H-205Tl spin-echo difference experiment we show that, in the Tl+-form of d(G4T4G4)2, small scalar couplings (<1 Hz) exist between 205Tl and protons in the G-quadruplex. These data comprise the first 1H-205Tl scalar couplings observed in a biological system and have the potential to provide important constraints for structure determination. These experiments can be applied to any system in which the substituted Tl+ cations are in slow exchange with the bulk ions in solution.
G4 notes
4 G-tetrads, 1 G4 helix, 1 G4 stem · (2+2), UDDU

Base-block schematics in six views [summary · tetrads · helices · stems · costacks · homepage]

PyMOL session file PDB file View in 3Dmol.js

List of 4 G-tetrads [summary · schematics · helices · stems · costacks · homepage]

 1 glyco-bond=s--s groove=w-n- planarity=0.339 type=other  nts=4 GGGG A.DG1,B.DG16,A.DG12,B.DG21
 2 glyco-bond=-ss- groove=w-n- planarity=0.098 type=planar nts=4 GGGG A.DG2,B.DG15,A.DG11,B.DG22
 3 glyco-bond=s--s groove=w-n- planarity=0.094 type=planar nts=4 GGGG A.DG3,B.DG14,A.DG10,B.DG23
 4 glyco-bond=-ss- groove=w-n- planarity=0.335 type=other  nts=4 GGGG A.DG4,B.DG13,A.DG9,B.DG24

List of 1 G4-helix [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.DG16,A.DG12,B.DG21
 2  glyco-bond=-ss- groove=w-n- WC-->Major nts=4 GGGG A.DG2,B.DG15,A.DG11,B.DG22
 3  glyco-bond=s--s groove=w-n- Major-->WC nts=4 GGGG A.DG3,B.DG14,A.DG10,B.DG23
 4  glyco-bond=-ss- groove=w-n- WC-->Major nts=4 GGGG A.DG4,B.DG13,A.DG9,B.DG24
  step#1  mm(<>,outward)  area=14.15 rise=3.30 twist=17.5
  step#2  pp(><,inward)   area=22.03 rise=2.80 twist=40.6
  step#3  mm(<>,outward)  area=14.15 rise=3.30 twist=17.5
  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.DG16,B.DG15,B.DG14,B.DG13
  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.DG21,B.DG22,B.DG23,B.DG24

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3 stacking diagrams
 1  glyco-bond=s--s groove=w-n- Major-->WC nts=4 GGGG A.DG1,B.DG16,A.DG12,B.DG21
2 glyco-bond=-ss- groove=w-n- WC-->Major nts=4 GGGG A.DG2,B.DG15,A.DG11,B.DG22
step#1 mm(<>,outward) area=14.15 rise=3.30 twist=17.5

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 2  glyco-bond=-ss- groove=w-n- WC-->Major nts=4 GGGG A.DG2,B.DG15,A.DG11,B.DG22
3 glyco-bond=s--s groove=w-n- Major-->WC nts=4 GGGG A.DG3,B.DG14,A.DG10,B.DG23
step#2 pp(><,inward) area=22.03 rise=2.80 twist=40.6

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 3  glyco-bond=s--s groove=w-n- Major-->WC nts=4 GGGG A.DG3,B.DG14,A.DG10,B.DG23
4 glyco-bond=-ss- groove=w-n- WC-->Major nts=4 GGGG A.DG4,B.DG13,A.DG9,B.DG24
step#3 mm(<>,outward) area=14.15 rise=3.30 twist=17.5

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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, 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.DG16,A.DG12,B.DG21
 2  glyco-bond=-ss- groove=w-n- WC-->Major nts=4 GGGG A.DG2,B.DG15,A.DG11,B.DG22
 3  glyco-bond=s--s groove=w-n- Major-->WC nts=4 GGGG A.DG3,B.DG14,A.DG10,B.DG23
 4  glyco-bond=-ss- groove=w-n- WC-->Major nts=4 GGGG A.DG4,B.DG13,A.DG9,B.DG24
  step#1  mm(<>,outward)  area=14.15 rise=3.30 twist=17.5
  step#2  pp(><,inward)   area=22.03 rise=2.80 twist=40.6
  step#3  mm(<>,outward)  area=14.15 rise=3.30 twist=17.5
  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.DG16,B.DG15,B.DG14,B.DG13
  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.DG21,B.DG22,B.DG23,B.DG24
  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.DT17,B.DT18,B.DT19,B.DT20

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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)