DSSR-enabled G4 identification/annotation: PDB entry 1evm
Summary information and primary citation
- 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, UUUU, parallel, 4+0
Cartoon-block schematics in six views (download the tarball)
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-tetrads, 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 |
| 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 |
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-tetrads, 0 loops, inter-molecular, UUUU, 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 |