DSSR-enabled G4 identification/annotation: PDB entry 2aqy
Summary information and primary citation
- PDB-id
- 2aqy
- Class
- DNA
- Method
- NMR
- Summary
- (3+1) assembly of three human telomeric DNA repeats into an asymmetrical dimeric g-quadruplex
- Reference
- Zhang N, Phan AT, Patel DJ (2005): "(3 + 1) Assembly of three human telomeric repeats into an asymmetric dimeric G-quadruplex." J.Am.Chem.Soc., 127, 17277-17285. doi: 10.1021/ja0543090.
- Abstract
- We present an NMR study on the structure of a DNA fragment of the human telomere containing three guanine-tracts, d(GGGTTAGGGTTAGGGT). This sequence forms in Na(+) solution a unique asymmetric dimeric quadruplex, in which the G-tetrad core involves all three G-tracts of one strand and only the last 3'-end G-tract of the other strand. We show that a three-repeat human telomeric sequence can also associate with a single-repeat human telomeric sequence into a structure with the same topology that we name (3 + 1) quadruplex assembly. In this G-quadruplex assembly, there are one syn.syn.syn.anti and two anti.anti.anti.syn G-tetrads, two edgewise loops, three G-tracts oriented in one direction and the fourth oriented in the opposite direction. We discuss the possible implications of the new folding topology for understanding the structure of telomeric DNA, including t-loop formation, and for targeting G-quadruplexes in the telomeres.
- G4 notes
- 3 G-tetrads, 1 G4 helix, 1 G4 stem, UUUD, hybrid2, 3+1
Cartoon-block schematics in six views (download the tarball)
List of 3 G-tetrads
1 glyco-bond=sss- sugar=3--- groove=--wn planarity=0.171 type=other -- nts=4 GGGG A.DG1,B.DG19,A.DG13,A.DG9 2 glyco-bond=---s sugar=---. groove=--wn planarity=0.220 type=other -- nts=4 gGGG A.DI2,B.DG20,A.DG14,A.DG8 3 glyco-bond=---s sugar=---- groove=--wn planarity=0.383 type=bowl -- nts=4 GGGG A.DG3,B.DG21,A.DG15,A.DG7
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
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1 glyco-bond=sss- sugar=3--- groove=--wn Major-->WC -- nts=4 GGGG A.DG1,B.DG19,A.DG13,A.DG9 2 glyco-bond=---s sugar=---. groove=--wn WC-->Major -- nts=4 gGGG A.DI2,B.DG20,A.DG14,A.DG8 3 glyco-bond=---s sugar=---- groove=--wn WC-->Major -- nts=4 GGGG A.DG3,B.DG21,A.DG15,A.DG7 step#1 mm(<>,outward) area=12.98 rise=3.71 twist=20.4 step#2 pm(>>,forward) area=12.91 rise=3.62 twist=27.5 strand#1 DNA glyco-bond=s-- sugar=3-- nts=3 GgG A.DG1,A.DI2,A.DG3 strand#2 DNA glyco-bond=s-- sugar=--- nts=3 GGG B.DG19,B.DG20,B.DG21 strand#3 DNA glyco-bond=s-- sugar=--- nts=3 GGG A.DG13,A.DG14,A.DG15 strand#4 DNA glyco-bond=-ss sugar=-.- nts=3 GGG A.DG9,A.DG8,A.DG7 |
| 2 stacking diagrams | |
|
1 glyco-bond=sss- sugar=3--- groove=--wn Major-->WC -- nts=4 GGGG A.DG1,B.DG19,A.DG13,A.DG9 |
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2 glyco-bond=---s sugar=---. groove=--wn WC-->Major -- nts=4 gGGG A.DI2,B.DG20,A.DG14,A.DG8 |
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, 2 loops, inter-molecular, UUUD, hybrid2, 3+1
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1 glyco-bond=sss- sugar=3--- groove=--wn Major-->WC -- nts=4 GGGG A.DG1,B.DG19,A.DG13,A.DG9 2 glyco-bond=---s sugar=---. groove=--wn WC-->Major -- nts=4 gGGG A.DI2,B.DG20,A.DG14,A.DG8 3 glyco-bond=---s sugar=---- groove=--wn WC-->Major -- nts=4 GGGG A.DG3,B.DG21,A.DG15,A.DG7 step#1 mm(<>,outward) area=12.98 rise=3.71 twist=20.4 step#2 pm(>>,forward) area=12.91 rise=3.62 twist=27.5 strand#1 U DNA glyco-bond=s-- sugar=3-- nts=3 GgG A.DG1,A.DI2,A.DG3 strand#2 U DNA glyco-bond=s-- sugar=--- nts=3 GGG B.DG19,B.DG20,B.DG21 strand#3 U DNA glyco-bond=s-- sugar=--- nts=3 GGG A.DG13,A.DG14,A.DG15 strand#4 D DNA glyco-bond=-ss sugar=-.- nts=3 GGG A.DG9,A.DG8,A.DG7 loop#1 type=lateral strands=[#1,#4] nts=3 TTA A.DT4,A.DT5,A.DA6 loop#2 type=lateral strands=[#4,#3] nts=3 TTA A.DT10,A.DT11,A.DA12 |