Detailed DSSR results for the G-quadruplex: PDB entry 2aqy
Created and maintained by Xiang-Jun Lu <xiangjun@x3dna.org>
Citation: Please cite the NAR'20 DSSR-PyMOL schematics paper and/or the NAR'15 DSSR method paper.
Summary information
- 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, (3+1), UUUD
Base-block schematics in six views
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=---3 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-tetrad layers, inter-molecular, with 1 stem
 |
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=---3 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=-3- 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 |
 |
2 glyco-bond=---s sugar=---3 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-tetrad layers, 2 loops, inter-molecular, UUUD, hybrid-(mixed), (3+1)
 |
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=---3 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=-3- 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 |