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PDB-id
1emq
Class
DNA
Method
NMR
Summary
NMR observation of t-tetrads in a parallel stranded DNA quadruplex formed by saccharomyces cerevisiae telomere repeats
Reference
Patel, P.K., Hosur, R.V.: (1999) "NMR observation of T-tetrads in a parallel stranded DNA quadruplex formed by Saccharomyces cerevisiae telomere repeats." Nucleic Acids Res., 27, 2457-2464.
Abstract
We report here the NMR structure of the DNA sequence d-TGGTGGC containing two repeats of Saccharomyces cerevisiae telomere DNA which is unique in that it has a single thymine in the repeat sequence and the number of Gs can vary from one to three. The structure is a novel quadruplex incor-porating T-tetrads formed by symmetrical pairing of four Ts via O4-H3 H-bonds in a plane. This is in contrast to the previous results on other telomeric sequences which contained more than one T in the repeat sequences and they were seen mostly in the flexible regions of the structures. We observed that the T4-tetrad was nicely accommodated in the center of the G-quadruplex, but it caused a small underwinding of the right handed helix. The T tetrad stacked well on the adjacent G3-tetrad, but poorly on the G5 tetrad. Likewise, T1 also formed a stable T-tetrad at the 5' end of the quadruplex. To our knowledge, this is the first report of T-tetrad formation in DNA structures. These observations are of significance from the points of view of both structural diversity and specific recognitions.
G4 notes
4 G-tetrads, 1 G4 helix, 2 G4 stems, 1 G4 coaxial stack · parallel(4+0), UUUU · coaxial interfaces: 3'/5'

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=---- groove=---- planarity=0.147 type=planar nts=4 GGGG A.DG102,C.DG402,D.DG302,B.DG202
 2 glyco-bond=---- groove=---- planarity=0.070 type=planar nts=4 GGGG A.DG103,C.DG403,D.DG303,B.DG203
 3 glyco-bond=---- groove=---- planarity=0.192 type=bowl   nts=4 GGGG A.DG105,C.DG405,D.DG305,B.DG205
 4 glyco-bond=---- groove=---- planarity=0.194 type=other  nts=4 GGGG A.DG106,C.DG406,D.DG306,B.DG206

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, inter-molecular, with 2 stems

 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG102,C.DG402,D.DG302,B.DG202
 2* glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG103,C.DG403,D.DG303,B.DG203
 3  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG A.DG105,B.DG205,D.DG305,C.DG405
 4  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG A.DG106,B.DG206,D.DG306,C.DG406
  step#1  pm(>>,forward)  area=12.06 rise=3.18 twist=29.9
  step#2  pm(>>,forward)  area=0.00  rise=6.76 twist=-32.0
  step#3  pm(>>,forward)  area=15.73 rise=3.06 twist=24.0
  strand#1 DNA glyco-bond=---- nts=4 GGGG A.DG102,A.DG103,A.DG105,A.DG106
  strand#2 DNA glyco-bond=---- nts=4 GGGG C.DG402,C.DG403,B.DG205,B.DG206
  strand#3 DNA glyco-bond=---- nts=4 GGGG D.DG302,D.DG303,D.DG305,D.DG306
  strand#4 DNA glyco-bond=---- nts=4 GGGG B.DG202,B.DG203,C.DG405,C.DG406

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3 stacking diagrams
 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG102,C.DG402,D.DG302,B.DG202
2* glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG103,C.DG403,D.DG303,B.DG203
step#1 pm(>>,forward) area=12.06 rise=3.18 twist=29.9

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 2* glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG103,C.DG403,D.DG303,B.DG203
3 glyco-bond=---- groove=---- Major-->WC nts=4 GGGG A.DG105,B.DG205,D.DG305,C.DG405
step#2 pm(>>,forward) area=0.00 rise=6.76 twist=-32.0

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 3  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG A.DG105,B.DG205,D.DG305,C.DG405
4 glyco-bond=---- groove=---- Major-->WC nts=4 GGGG A.DG106,B.DG206,D.DG306,C.DG406
step#3 pm(>>,forward) area=15.73 rise=3.06 twist=24.0

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List of 2 G4-stems [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, 2 G-tetrad layers, 0 loops, inter-molecular, UUUU, parallel, parallel(4+0)

 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG102,C.DG402,D.DG302,B.DG202
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG103,C.DG403,D.DG303,B.DG203
  step#1  pm(>>,forward)  area=12.06 rise=3.18 twist=29.9
  strand#1  U DNA glyco-bond=-- nts=2 GG A.DG102,A.DG103
  strand#2  U DNA glyco-bond=-- nts=2 GG C.DG402,C.DG403
  strand#3  U DNA glyco-bond=-- nts=2 GG D.DG302,D.DG303
  strand#4  U DNA glyco-bond=-- nts=2 GG B.DG202,B.DG203

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Stem#2, 2 G-tetrad layers, 0 loops, inter-molecular, UUUU, parallel, parallel(4+0)

 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG105,C.DG405,D.DG305,B.DG205
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG106,C.DG406,D.DG306,B.DG206
  step#1  pm(>>,forward)  area=15.73 rise=3.06 twist=24.0
  strand#1  U DNA glyco-bond=-- nts=2 GG A.DG105,A.DG106
  strand#2  U DNA glyco-bond=-- nts=2 GG C.DG405,C.DG406
  strand#3  U DNA glyco-bond=-- nts=2 GG D.DG305,D.DG306
  strand#4  U DNA glyco-bond=-- nts=2 GG B.DG205,B.DG206

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List of 1 G4 coaxial stack [summary · schematics · tetrads · helices · stems · homepage]

 1 G4 helix#1 contains 2 G4 stems: [#1,#2]  [3'/5']

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