Summary information

PDB id
1aff
Class
DNA
Method
NMR
Summary
DNA quadruplex containing gggg tetrads and (t.a).a triads, NMR, 8 structures
Reference
Kettani A, Bouaziz S, Wang W, Jones RA, Patel DJ (1997): "Bombyx mori single repeat telomeric DNA sequence forms a G-quadruplex capped by base triads." Nat.Struct.Biol., 4, 382-389. doi: 10.1038/nsb0597-382.
Abstract
A combined NMR-molecular dynamics approach has been applied to determine the solution structure of a truncated analogue of the Bombyx mori telomeric d(TTAGG) single repeat sequence in Na+ cation-containing aqueous solution. The two-fold symmetric four-stranded d(TAGG) quadruplex contains two adjacent G(syn).G(syn).G(anti).G(anti) G-tetrads sandwiched between novel (T.A).A triads with individual strands having both a parallel and antiparallel neighbour around the quadruplex. The (T.A).A triad represents the first experimental verification of a base triad alignment which constitutes a key postulate in the recently proposed model of triad-DNA. Further, the (T.A).A triad is generated by positioning an A residue through hydrogen bonding in the minor groove of a Watson-Crick T.A base pair and includes a T-A platform related to an A-A platform recently observed in the structure of the P4-P6 domain of the Tetrahymena self splicing group I ribozyme. The novel architecture of the truncated Bombyx mori quadruplex structure sets the stage for the design and potential identification of additional base tetrads and triads that could participate in pairing alignments of multi-stranded DNA structures during chromosome association and genetic recombination.
G4 notes
2 G-tetrads, 1 G4 helix, 1 G4 stem, (2+2), UUDD

Base-block schematics in six views

PyMOL session file PDB file View in 3Dmol.js

List of 2 G-tetrads

 1 glyco-bond=ss-- sugar=---- groove=-w-n planarity=0.543 type=other  nts=4 GGGG A.DG3,B.DG3,D.DG4,C.DG4
 2 glyco-bond=--ss sugar=---- groove=-w-n planarity=0.544 type=other  nts=4 GGGG A.DG4,B.DG4,D.DG3,C.DG3

List of 1 G4-helix

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

 1  glyco-bond=ss-- sugar=---- groove=-w-n Major-->WC nts=4 GGGG A.DG3,B.DG3,D.DG4,C.DG4
 2  glyco-bond=--ss sugar=---- groove=-w-n WC-->Major nts=4 GGGG A.DG4,B.DG4,D.DG3,C.DG3
  step#1  mm(<>,outward)  area=15.61 rise=3.44 twist=18.6
  strand#1 DNA glyco-bond=s- sugar=-- nts=2 GG A.DG3,A.DG4
  strand#2 DNA glyco-bond=s- sugar=-- nts=2 GG B.DG3,B.DG4
  strand#3 DNA glyco-bond=-s sugar=-- nts=2 GG D.DG4,D.DG3
  strand#4 DNA glyco-bond=-s sugar=-- nts=2 GG C.DG4,C.DG3

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1 stacking diagram 
 1  glyco-bond=ss-- sugar=---- groove=-w-n Major-->WC nts=4 GGGG A.DG3,B.DG3,D.DG4,C.DG4
 2  glyco-bond=--ss sugar=---- groove=-w-n WC-->Major nts=4 GGGG A.DG4,B.DG4,D.DG3,C.DG3
  step#1  mm(<>,outward)  area=15.61 rise=3.44 twist=18.6

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List of 1 G4-stem

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, 0 loops, inter-molecular, UUDD, anti-parallel, (2+2)

 1  glyco-bond=ss-- sugar=---- groove=-w-n Major-->WC nts=4 GGGG A.DG3,B.DG3,D.DG4,C.DG4
 2  glyco-bond=--ss sugar=---- groove=-w-n WC-->Major nts=4 GGGG A.DG4,B.DG4,D.DG3,C.DG3
  step#1  mm(<>,outward)  area=15.61 rise=3.44 twist=18.6
  strand#1  U DNA glyco-bond=s- sugar=-- nts=2 GG A.DG3,A.DG4
  strand#2  U DNA glyco-bond=s- sugar=-- nts=2 GG B.DG3,B.DG4
  strand#3  D DNA glyco-bond=-s sugar=-- nts=2 GG D.DG4,D.DG3
  strand#4  D DNA glyco-bond=-s sugar=-- nts=2 GG C.DG4,C.DG3

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