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

PDB-id
201d
Class
DNA
Method
NMR
Summary
Solution structure of the oxytricha telomeric repeat d[g4(t4g4)3] G-tetraplex
Reference
Wang, Y., Patel, D.J.: (1995) "Solution structure of the Oxytricha telomeric repeat d[G4(T4G4)3] G-tetraplex." J.Mol.Biol., 251, 76-94.
Abstract
The solution structure of Oxytricha telomere sequence d[G4(T4G4)3] in 0.1 M Na+ containing solution has been determined using a combined NMR-molecular dynamics approach including relaxation matrix refinement. This four G4 repeat sequence folds intramolecularly into a right-handed G-tetraplex containing four stacked G-tetrads which are connected by two lateral T4 loops and a central diagonal T4 loop. The guanine glycosidic bonds adopt a syn-anti alternation along the full length of the d[G4(T4G4)3] sequence while the orientation around adjacent G-tetrads switches between syn.syn.anti.anti and anti.anti.syn.syn alignments. Four distinct grooves are formed by the parallel (two of medium width) and anti-parallel (one wide and one narrow width) alignment of adjacent G-G-G-G segments in the G-tetraplex. The T4 residues in the diagonal loop are well-defined while the T4 residues in both lateral loops are under-defined and sample multiple conformations. The solution structure of the Na(+)-stabilized Oxytricha d[G4(T4G4)3] G-tetraplex and an earlier solution structure reported from our laboratory on the Na(+)-stabilized human d[AG3(T2AG3)3] G-tetraplex exhibit a common folding topology defined by the same syn/anti distribution of guanine residues along individual strands and around individual G-tetrads, as well as a common central diagonal loop which defines the strand directionalities. The well-resolved proton NMR spectra associated with the d[G4(T4G4)3] G-tetraplex opens the opportunity for studies ranging from cation-dependent characterization of G-tetraplex conformation and hydration to ligand and protein recognition of the distinct grooves associated with this folding topology.
G4 notes
4 G-tetrads, 1 G4 helix, 1 G4 stem · 4(-LwD+Ln), basket(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=0.464 type=bowl   nts=4 GGGG A.DG1,A.DG12,A.DG28,A.DG17
 2 glyco-bond=-ss- groove=w-n- planarity=0.250 type=other  nts=4 GGGG A.DG2,A.DG11,A.DG27,A.DG18
 3 glyco-bond=s--s groove=w-n- planarity=0.205 type=other  nts=4 GGGG A.DG3,A.DG10,A.DG26,A.DG19
 4 glyco-bond=-ss- groove=w-n- planarity=0.290 type=other  nts=4 GGGG A.DG4,A.DG9,A.DG25,A.DG20

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, INTRA-molecular, with 1 stem

 1  glyco-bond=s--s groove=w-n- Major-->WC nts=4 GGGG A.DG1,A.DG12,A.DG28,A.DG17
 2  glyco-bond=-ss- groove=w-n- WC-->Major nts=4 GGGG A.DG2,A.DG11,A.DG27,A.DG18
 3  glyco-bond=s--s groove=w-n- Major-->WC nts=4 GGGG A.DG3,A.DG10,A.DG26,A.DG19
 4  glyco-bond=-ss- groove=w-n- WC-->Major nts=4 GGGG A.DG4,A.DG9,A.DG25,A.DG20
  step#1  mm(<>,outward)  area=11.71 rise=3.61 twist=19.1
  step#2  pp(><,inward)   area=17.57 rise=3.65 twist=37.2
  step#3  mm(<>,outward)  area=11.76 rise=3.75 twist=17.6
  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 A.DG12,A.DG11,A.DG10,A.DG9
  strand#3 DNA glyco-bond=-s-s nts=4 GGGG A.DG28,A.DG27,A.DG26,A.DG25
  strand#4 DNA glyco-bond=s-s- nts=4 GGGG A.DG17,A.DG18,A.DG19,A.DG20

Download PDB file
Interactive view in 3Dmol.js

3 stacking diagrams
 1  glyco-bond=s--s groove=w-n- Major-->WC nts=4 GGGG A.DG1,A.DG12,A.DG28,A.DG17
2 glyco-bond=-ss- groove=w-n- WC-->Major nts=4 GGGG A.DG2,A.DG11,A.DG27,A.DG18
step#1 mm(<>,outward) area=11.71 rise=3.61 twist=19.1

Download PDB file
Interactive view in 3Dmol.js

 2  glyco-bond=-ss- groove=w-n- WC-->Major nts=4 GGGG A.DG2,A.DG11,A.DG27,A.DG18
3 glyco-bond=s--s groove=w-n- Major-->WC nts=4 GGGG A.DG3,A.DG10,A.DG26,A.DG19
step#2 pp(><,inward) area=17.57 rise=3.65 twist=37.2

Download PDB file
Interactive view in 3Dmol.js

 3  glyco-bond=s--s groove=w-n- Major-->WC nts=4 GGGG A.DG3,A.DG10,A.DG26,A.DG19
4 glyco-bond=-ss- groove=w-n- WC-->Major nts=4 GGGG A.DG4,A.DG9,A.DG25,A.DG20
step#3 mm(<>,outward) area=11.76 rise=3.75 twist=17.6

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, 4 G-tetrad layers, 3 loops, INTRA-molecular, UDDU, anti-parallel, 4(-LwD+Ln), basket(2+2)

 1  glyco-bond=s--s groove=w-n- Major-->WC nts=4 GGGG A.DG1,A.DG12,A.DG28,A.DG17
 2  glyco-bond=-ss- groove=w-n- WC-->Major nts=4 GGGG A.DG2,A.DG11,A.DG27,A.DG18
 3  glyco-bond=s--s groove=w-n- Major-->WC nts=4 GGGG A.DG3,A.DG10,A.DG26,A.DG19
 4  glyco-bond=-ss- groove=w-n- WC-->Major nts=4 GGGG A.DG4,A.DG9,A.DG25,A.DG20
  step#1  mm(<>,outward)  area=11.71 rise=3.61 twist=19.1
  step#2  pp(><,inward)   area=17.57 rise=3.65 twist=37.2
  step#3  mm(<>,outward)  area=11.76 rise=3.75 twist=17.6
  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 A.DG12,A.DG11,A.DG10,A.DG9
  strand#3  D DNA glyco-bond=-s-s nts=4 GGGG A.DG28,A.DG27,A.DG26,A.DG25
  strand#4  U DNA glyco-bond=s-s- nts=4 GGGG A.DG17,A.DG18,A.DG19,A.DG20
  loop#1 type=lateral   strands=[#1,#2] nts=4 TTTT A.DT5,A.DT6,A.DT7,A.DT8
  loop#2 type=diagonal  strands=[#2,#4] nts=4 TTTT A.DT13,A.DT14,A.DT15,A.DT16
  loop#3 type=lateral   strands=[#4,#3] nts=4 TTTT A.DT21,A.DT22,A.DT23,A.DT24

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)