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

PDB-id
1evn
Class
DNA
Method
NMR
Summary
NMR observation of a-tetrad
Reference
Patel, P.K., Koti, A.S., Hosur, R.V.: (1999) "NMR studies on truncated sequences of human telomeric DNA: observation of a novel A-tetrad." Nucleic Acids Res., 27, 3836-3843.
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 [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=---- groove=---- planarity=0.160 type=planar nts=4 GGGG M.DG102,P.DG402,O.DG302,N.DG202
 2 glyco-bond=---- groove=---- planarity=0.291 type=bowl   nts=4 GGGG M.DG103,P.DG403,O.DG303,N.DG203
 3 glyco-bond=---- groove=---- planarity=0.297 type=bowl   nts=4 GGGG M.DG104,P.DG404,O.DG304,N.DG204

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, inter-molecular, with 1 stem

 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG M.DG102,P.DG402,O.DG302,N.DG202
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG M.DG103,P.DG403,O.DG303,N.DG203
 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG M.DG104,P.DG404,O.DG304,N.DG204
  step#1  pm(>>,forward)  area=17.89 rise=3.23 twist=20.1
  step#2  pm(>>,forward)  area=8.63  rise=3.16 twist=32.0
  strand#1 DNA glyco-bond=--- nts=3 GGG M.DG102,M.DG103,M.DG104
  strand#2 DNA glyco-bond=--- nts=3 GGG P.DG402,P.DG403,P.DG404
  strand#3 DNA glyco-bond=--- nts=3 GGG O.DG302,O.DG303,O.DG304
  strand#4 DNA glyco-bond=--- nts=3 GGG N.DG202,N.DG203,N.DG204

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2 stacking diagrams
 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG M.DG102,P.DG402,O.DG302,N.DG202
2 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG M.DG103,P.DG403,O.DG303,N.DG203
step#1 pm(>>,forward) area=17.89 rise=3.23 twist=20.1

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 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG M.DG103,P.DG403,O.DG303,N.DG203
3 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG M.DG104,P.DG404,O.DG304,N.DG204
step#2 pm(>>,forward) area=8.63 rise=3.16 twist=32.0

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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, 0 loops, inter-molecular, UUUU, parallel, parallel(4+0)

 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG M.DG102,P.DG402,O.DG302,N.DG202
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG M.DG103,P.DG403,O.DG303,N.DG203
 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG M.DG104,P.DG404,O.DG304,N.DG204
  step#1  pm(>>,forward)  area=17.89 rise=3.23 twist=20.1
  step#2  pm(>>,forward)  area=8.63  rise=3.16 twist=32.0
  strand#1  U DNA glyco-bond=--- nts=3 GGG M.DG102,M.DG103,M.DG104
  strand#2  U DNA glyco-bond=--- nts=3 GGG P.DG402,P.DG403,P.DG404
  strand#3  U DNA glyco-bond=--- nts=3 GGG O.DG302,O.DG303,O.DG304
  strand#4  U DNA glyco-bond=--- nts=3 GGG N.DG202,N.DG203,N.DG204

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

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