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

PDB-id
186d
Class
DNA
Method
NMR
Summary
Solution structure of the tetrahymena telomeric repeat d(t2g4)4 G-tetraplex
Reference
Wang, Y., Patel, D.J.: (1994) "Solution structure of the Tetrahymena telomeric repeat d(T2G4)4 G-tetraplex." Structure, 2, 1141-1156.
Abstract
Telomeres in eukaryotic organisms are protein-DNA complexes which are essential for the protection and replication of chromosomal termini. The telomeric DNA of Tetrahymena consists of T2G4 repeats, and models have been previously proposed for the intramolecular folded structure of the d(T2G4)4 sequence based on chemical footprinting and cross-linking data. A high-resolution solution structure of this sequence would allow comparison with the structures of related G-tetraplexes.
The solution structure of the Na(+)-stabilized d(T2G4)4 sequence has been determined using a combined NMR-molecular dynamics approach. The sequence folds intramolecularly into a right-handed G-tetraplex containing three stacked G-tetrads connected by linker segments consisting of a G-T-T-G lateral loop, a central T-T-G lateral loop and a T-T segment that spans the groove through a double chain reversal. The latter T-T connectivity aligns adjacent G-G-G segments in parallel and introduces a new G-tetraplex folding topology with unprecedented combinations of strand directionalities and groove widths, as well as guanine syn/anti distributions along individual strands and around individual G-tetrads.
The four repeat Tetrahymena and human G-tetraplexes, which differ by a single guanine for adenine substitution, exhibit strikingly different folding topologies. The observed structural polymorphism establishes that G-tetraplexes can adopt topologies which project distinctly different groove dimensions, G-tetrad base edges and linker segments for recognition by, and interactions with, other nucleic acids and proteins.
G4 notes
3 G-tetrads, 1 G4 helix, 1 G4 stem · 3(-Lw-Ln-P), hybrid-2(3+1), UDUU

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

PyMOL session file PDB file View in 3Dmol.js

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

 1 glyco-bond=s-ss groove=wn-- planarity=0.418 type=other  nts=4 GGGG A.DG3,A.DG12,A.DG16,A.DG21
 2 glyco-bond=-s-- groove=wn-- planarity=0.445 type=other  nts=4 GGGG A.DG4,A.DG11,A.DG17,A.DG22
 3 glyco-bond=-s-- groove=wn-- planarity=0.333 type=other  nts=4 GGGG A.DG5,A.DG10,A.DG18,A.DG23

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, INTRA-molecular, with 1 stem

 1  glyco-bond=s-ss groove=wn-- Major-->WC nts=4 GGGG A.DG3,A.DG12,A.DG16,A.DG21
 2  glyco-bond=-s-- groove=wn-- WC-->Major nts=4 GGGG A.DG4,A.DG11,A.DG17,A.DG22
 3  glyco-bond=-s-- groove=wn-- WC-->Major nts=4 GGGG A.DG5,A.DG10,A.DG18,A.DG23
  step#1  mm(<>,outward)  area=10.30 rise=3.41 twist=20.5
  step#2  pm(>>,forward)  area=11.83 rise=3.36 twist=28.1
  strand#1 DNA glyco-bond=s-- nts=3 GGG A.DG3,A.DG4,A.DG5
  strand#2 DNA glyco-bond=-ss nts=3 GGG A.DG12,A.DG11,A.DG10
  strand#3 DNA glyco-bond=s-- nts=3 GGG A.DG16,A.DG17,A.DG18
  strand#4 DNA glyco-bond=s-- nts=3 GGG A.DG21,A.DG22,A.DG23

Download PDB file
Interactive view in 3Dmol.js

2 stacking diagrams
 1  glyco-bond=s-ss groove=wn-- Major-->WC nts=4 GGGG A.DG3,A.DG12,A.DG16,A.DG21
2 glyco-bond=-s-- groove=wn-- WC-->Major nts=4 GGGG A.DG4,A.DG11,A.DG17,A.DG22
step#1 mm(<>,outward) area=10.30 rise=3.41 twist=20.5

Download PDB file
Interactive view in 3Dmol.js

 2  glyco-bond=-s-- groove=wn-- WC-->Major nts=4 GGGG A.DG4,A.DG11,A.DG17,A.DG22
3 glyco-bond=-s-- groove=wn-- WC-->Major nts=4 GGGG A.DG5,A.DG10,A.DG18,A.DG23
step#2 pm(>>,forward) area=11.83 rise=3.36 twist=28.1

Download PDB file
Interactive view in 3Dmol.js

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, 3 loops, INTRA-molecular, UDUU, anti-parallel, 3(-Lw-Ln-P), hybrid-2(3+1)

 1  glyco-bond=s-ss groove=wn-- Major-->WC nts=4 GGGG A.DG3,A.DG12,A.DG16,A.DG21
 2  glyco-bond=-s-- groove=wn-- WC-->Major nts=4 GGGG A.DG4,A.DG11,A.DG17,A.DG22
 3  glyco-bond=-s-- groove=wn-- WC-->Major nts=4 GGGG A.DG5,A.DG10,A.DG18,A.DG23
  step#1  mm(<>,outward)  area=10.30 rise=3.41 twist=20.5
  step#2  pm(>>,forward)  area=11.83 rise=3.36 twist=28.1
  strand#1  U DNA glyco-bond=s-- nts=3 GGG A.DG3,A.DG4,A.DG5
  strand#2  D DNA glyco-bond=-ss nts=3 GGG A.DG12,A.DG11,A.DG10
  strand#3  U DNA glyco-bond=s-- nts=3 GGG A.DG16,A.DG17,A.DG18
  strand#4  U DNA glyco-bond=s-- nts=3 GGG A.DG21,A.DG22,A.DG23
  loop#1 type=lateral   strands=[#1,#2] nts=4 GTTG A.DG6,A.DT7,A.DT8,A.DG9
  loop#2 type=lateral   strands=[#2,#3] nts=3 TTG A.DT13,A.DT14,A.DG15
  loop#3 type=propeller strands=[#3,#4] nts=2 TT A.DT19,A.DT20

Download PDB file
Interactive view in 3Dmol.js

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

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