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

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, A.T., Patel, D.J.: (2005) "(3 + 1) Assembly of three human telomeric repeats into an asymmetric dimeric G-quadruplex." J.Am.Chem.Soc., 127, 17277-17285.
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 [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=sss- groove=--wn planarity=0.171 type=other  nts=4 GGGG A.DG1,B.DG19,A.DG13,A.DG9
 2 glyco-bond=---s groove=--wn planarity=0.220 type=other  nts=4 gGGG A.DI2,B.DG20,A.DG14,A.DG8
 3 glyco-bond=---s groove=--wn planarity=0.383 type=bowl   nts=4 GGGG A.DG3,B.DG21,A.DG15,A.DG7

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=sss- groove=--wn Major-->WC nts=4 GGGG A.DG1,B.DG19,A.DG13,A.DG9
 2  glyco-bond=---s groove=--wn WC-->Major nts=4 gGGG A.DI2,B.DG20,A.DG14,A.DG8
 3  glyco-bond=---s 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-- nts=3 GgG A.DG1,A.DI2,A.DG3
  strand#2 DNA glyco-bond=s-- nts=3 GGG B.DG19,B.DG20,B.DG21
  strand#3 DNA glyco-bond=s-- nts=3 GGG A.DG13,A.DG14,A.DG15
  strand#4 DNA glyco-bond=-ss nts=3 GGG A.DG9,A.DG8,A.DG7

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2 stacking diagrams
 1  glyco-bond=sss- groove=--wn Major-->WC nts=4 GGGG A.DG1,B.DG19,A.DG13,A.DG9
2 glyco-bond=---s groove=--wn WC-->Major nts=4 gGGG A.DI2,B.DG20,A.DG14,A.DG8
step#1 mm(<>,outward) area=12.98 rise=3.71 twist=20.4

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 2  glyco-bond=---s groove=--wn WC-->Major nts=4 gGGG A.DI2,B.DG20,A.DG14,A.DG8
3 glyco-bond=---s groove=--wn WC-->Major nts=4 GGGG A.DG3,B.DG21,A.DG15,A.DG7
step#2 pm(>>,forward) area=12.91 rise=3.62 twist=27.5

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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, 2 loops, inter-molecular, UUUD, anti-parallel, (3+1)

 1  glyco-bond=sss- groove=--wn Major-->WC nts=4 GGGG A.DG1,B.DG19,A.DG13,A.DG9
 2  glyco-bond=---s groove=--wn WC-->Major nts=4 gGGG A.DI2,B.DG20,A.DG14,A.DG8
 3  glyco-bond=---s 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-- nts=3 GgG A.DG1,A.DI2,A.DG3
  strand#2  U DNA glyco-bond=s-- nts=3 GGG B.DG19,B.DG20,B.DG21
  strand#3  U DNA glyco-bond=s-- nts=3 GGG A.DG13,A.DG14,A.DG15
  strand#4  D DNA glyco-bond=-ss 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

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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)