Summary information

PDB id
1evm
Class
DNA
Method
NMR
Summary
NMR observation of a-tetrad
Reference
Patel PK, Koti AS, Hosur RV (1999): "NMR studies on truncated sequences of human telomeric DNA: observation of a novel A-tetrad." Nucleic Acids Res., 27, 3836-3843. doi: 10.1093/nar/27.19.3836.
Abstract
The structure of the telomeric DNA has been a subject of extensive investigation in recent years due to the realization that it has important functional roles to play in vivo and the observations that truncated telomeric sequences exhibit a great variety of 3D structures in aqueous solutions. In this context, we describe here NMR structural studies on two truncated human telomeric DNA sequences, d-AG(3)T and d-TAG(3)T in solutions containing K(+)ions. The G(3)stretches in both the oligonucleotides were seen to form parallel-stranded quadruplexes. However, the AG(3)segment as a whole, had different structural characteristics. The structure of d-AG(3)T revealed the formation of a novel A-tetrad, which was not seen in d-TAG(3)T. The A's in the tetrad had syn glycosidic conformation as opposed to the anti conformation of the G's in the G-tetrads. The A-tetrad stacked well over the adjacent G-tetrad and the twist angle at this step was smaller in d-AG(3)T than in d-TAG(3)T. These observations are expected to be significant from the point of view of structural diversity and recognition in telomeres.
G4 notes
3 G-tetrads, 1 G4 helix, 1 G4 stem, parallel(4+0), UUUU

Base-block schematics in six views

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List of 3 G-tetrads

 1 glyco-bond=---- sugar=---- groove=---- planarity=0.175 type=bowl-2 nts=4 GGGG M.DG302,P.DG402,O.DG302,N.DG402
 2 glyco-bond=---- sugar=---- groove=---- planarity=0.320 type=bowl   nts=4 GGGG M.DG303,P.DG403,O.DG303,N.DG403
 3 glyco-bond=---- sugar=---- groove=---- planarity=0.321 type=bowl   nts=4 GGGG M.DG304,P.DG404,O.DG304,N.DG404

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

 1  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG M.DG302,P.DG402,O.DG302,N.DG402
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG M.DG303,P.DG403,O.DG303,N.DG403
 3  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG M.DG304,P.DG404,O.DG304,N.DG404
  step#1  pm(>>,forward)  area=16.39 rise=3.24 twist=20.9
  step#2  pm(>>,forward)  area=8.12  rise=3.18 twist=32.7
  strand#1 DNA glyco-bond=--- sugar=--- nts=3 GGG M.DG302,M.DG303,M.DG304
  strand#2 DNA glyco-bond=--- sugar=--- nts=3 GGG P.DG402,P.DG403,P.DG404
  strand#3 DNA glyco-bond=--- sugar=--- nts=3 GGG O.DG302,O.DG303,O.DG304
  strand#4 DNA glyco-bond=--- sugar=--- nts=3 GGG N.DG402,N.DG403,N.DG404

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2 stacking diagrams
 1  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG M.DG302,P.DG402,O.DG302,N.DG402
2 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG M.DG303,P.DG403,O.DG303,N.DG403
step#1 pm(>>,forward) area=16.39 rise=3.24 twist=20.9

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 2  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG M.DG303,P.DG403,O.DG303,N.DG403
3 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG M.DG304,P.DG404,O.DG304,N.DG404
step#2 pm(>>,forward) area=8.12 rise=3.18 twist=32.7

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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, 3 G-tetrad layers, 0 loops, inter-molecular, UUUU, parallel, parallel(4+0)

 1  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG M.DG302,P.DG402,O.DG302,N.DG402
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG M.DG303,P.DG403,O.DG303,N.DG403
 3  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG M.DG304,P.DG404,O.DG304,N.DG404
  step#1  pm(>>,forward)  area=16.39 rise=3.24 twist=20.9
  step#2  pm(>>,forward)  area=8.12  rise=3.18 twist=32.7
  strand#1  U DNA glyco-bond=--- sugar=--- nts=3 GGG M.DG302,M.DG303,M.DG304
  strand#2  U DNA glyco-bond=--- sugar=--- nts=3 GGG P.DG402,P.DG403,P.DG404
  strand#3  U DNA glyco-bond=--- sugar=--- nts=3 GGG O.DG302,O.DG303,O.DG304
  strand#4  U DNA glyco-bond=--- sugar=--- nts=3 GGG N.DG402,N.DG403,N.DG404

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