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

PDB-id
1u64
Class
DNA
Method
NMR
Summary
The solution structure of d(g3t4g4)2
Reference
Sket, P., Crnugelj, M., Plavec, J.: (2004) "d(G3T4G4) forms unusual dimeric G-quadruplex structure with the same general fold in the presence of K+, Na+ or NH4+ ions." Bioorg.Med.Chem., 12, 5735-5744.
Abstract
We have recently communicated that DNA oligonucleotide d(G(3)T(4)G(4)) forms a dimeric G-quadruplex in the presence of K(+) ions [J. Am. Chem. Soc.2003, 125, 7866-7871]. The high-resolution NMR structure of d(G(3)T(4)G(4))(2) G-quadruplex exhibits G-quadruplex core consisting of three stacked G-quartets. The two overhanging G3 and G11 residues are located at the opposite sides of the end G-quartets and are not involved in G-quartet formation. d(G(3)T(4)G(4))(2) G-quadruplex represents the first bimolecular G-quadruplex where end G-quartets are spanned by diagonal (T4-T7) as well as edge-type loops (T15-T18). Three of the G-rich strands are parallel while one is anti-parallel. The G12-G22 strand demonstrates a sharp reversal in strand direction between residues G19 and G20 that is accommodated with the leap over the middle G-quartet. The reversal in strand direction is achieved without any extra intervening residues. Here we furthermore examined the influence of different monovalent cations on the folding of d(G(3)T(4)G(4)). The resolved imino and aromatic proton resonances as well as (sequential) NOE connectivity patterns showed only minor differences in key intra- and interquartet NOE intensities in the presence of K(+), Na(+) and NH(4)(+) ions, which were consistent with subtle structural differences while retaining the same folding topology of d(G(3)T(4)G(4))(2) G-quadruplex.
G4 notes
3 G-tetrads, 1 G4 helix, 1 G4 stem · (1+3), UDDD

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

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List of 3 G-tetrads [summary · schematics · helices · stems · costacks · homepage]

 1 glyco-bond=s--- groove=w--n planarity=0.178 type=other  nts=4 GGGG A.DG1,B.DG13,A.DG9,B.DG21
 2 glyco-bond=-sss groove=w--n planarity=0.240 type=other  nts=4 GGGG A.DG2,B.DG12,A.DG8,B.DG20
 3 glyco-bond=--s- groove=-wn- planarity=0.263 type=other  nts=4 GGGG A.DG10,B.DG14,B.DG19,B.DG22

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

 1  glyco-bond=-sss groove=w--n WC-->Major nts=4 GGGG A.DG2,B.DG12,A.DG8,B.DG20
 2  glyco-bond=s--- groove=w--n Major-->WC nts=4 GGGG A.DG1,B.DG13,A.DG9,B.DG21
 3  glyco-bond=s--- groove=w--n Major-->WC nts=4 GGGG B.DG19,B.DG14,A.DG10,B.DG22
  step#1  mm(<>,outward)  area=10.19 rise=3.37 twist=29.3
  step#2  pm(>>,forward)  area=14.79 rise=3.27 twist=27.1
  strand#1 DNA glyco-bond=-ss nts=3 GGG A.DG2,A.DG1,B.DG19
  strand#2 DNA glyco-bond=s-- nts=3 GGG B.DG12,B.DG13,B.DG14
  strand#3 DNA glyco-bond=s-- nts=3 GGG A.DG8,A.DG9,A.DG10
  strand#4 DNA glyco-bond=s-- nts=3 GGG B.DG20,B.DG21,B.DG22

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2 stacking diagrams
 1  glyco-bond=-sss groove=w--n WC-->Major nts=4 GGGG A.DG2,B.DG12,A.DG8,B.DG20
2 glyco-bond=s--- groove=w--n Major-->WC nts=4 GGGG A.DG1,B.DG13,A.DG9,B.DG21
step#1 mm(<>,outward) area=10.19 rise=3.37 twist=29.3

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 2  glyco-bond=s--- groove=w--n Major-->WC nts=4 GGGG A.DG1,B.DG13,A.DG9,B.DG21
3 glyco-bond=s--- groove=w--n Major-->WC nts=4 GGGG B.DG19,B.DG14,A.DG10,B.DG22
step#2 pm(>>,forward) area=14.79 rise=3.27 twist=27.1

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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, 2 G-tetrad layers, 2 loops, inter-molecular, UDDD, anti-parallel, (1+3)

 1  glyco-bond=s--- groove=w--n Major-->WC nts=4 GGGG A.DG1,B.DG13,A.DG9,B.DG21
 2  glyco-bond=-sss groove=w--n WC-->Major nts=4 GGGG A.DG2,B.DG12,A.DG8,B.DG20
  step#1  mm(<>,outward)  area=10.19 rise=3.37 twist=29.3
  strand#1  U DNA glyco-bond=s- nts=2 GG A.DG1,A.DG2
  strand#2  D DNA glyco-bond=-s nts=2 GG B.DG13,B.DG12
  strand#3  D DNA glyco-bond=-s nts=2 GG A.DG9,A.DG8
  strand#4  D DNA glyco-bond=-s nts=2 GG B.DG21,B.DG20
  loop#1 type=diagonal  strands=[#1,#3] nts=5 GTTTT A.DG3,A.DT4,A.DT5,A.DT6,A.DT7
  loop#2 type=diag-prop strands=[#2,#4] nts=6 GTTTTG B.DG14,B.DT15,B.DT16,B.DT17,B.DT18,B.DG19

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

List of 2 non-stem G4-loops (including the two closing Gs)

 1 type=lateral   helix=#1 nts=6 GTTTTG B.DG14,B.DT15,B.DT16,B.DT17,B.DT18,B.DG19
 2 type=V-shaped  helix=#1 nts=4 GGGG B.DG19,B.DG20,B.DG21,B.DG22