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PDB-id
2kow
Class
DNA
Method
NMR
Summary
Structure of a two-G-tetrad basket-type intramolecular G-quadruplex formed by giardia telomeric repeat d(taggg)4 in k+ solution (with g18-to-ino substitution)
Reference
Hu, L., Lim, K.W., Bouaziz, S., Phan, A.T.: (2009) "Giardia Telomeric Sequence d(TAGGG)(4) Forms Two Intramolecular G-Quadruplexes in K(+) Solution: Effect of Loop Length and Sequence on the Folding Topology." J.Am.Chem.Soc., 131, 16824-16831.
Abstract
Recently, it has been shown that in K(+) solution the human telomeric sequence d[TAGGG(TTAGGG)(3)] forms a (3 + 1) intramolecular G-quadruplex, while the Bombyx mori telomeric sequence d[TAGG(TTAGG)(3)], which differs from the human counterpart only by one G deletion in each repeat, forms a chair-type intramolecular G-quadruplex, indicating an effect of G-tract length on the folding topology of G-quadruplexes. To explore the effect of loop length and sequence on the folding topology of G-quadruplexes, here we examine the structure of the four-repeat Giardia telomeric sequence d[TAGGG(TAGGG)(3)], which differs from the human counterpart only by one T deletion within the non-G linker in each repeat. We show by NMR that this sequence forms two different intramolecular G-quadruplexes in K(+) solution. The first one is a novel basket-type antiparallel-stranded G-quadruplex containing two G-tetrads, a G x (A-G) triad, and two A x T base pairs; the three loops are consecutively edgewise-diagonal-edgewise. The second one is a propeller-type parallel-stranded G-quadruplex involving three G-tetrads; the three loops are all double-chain-reversal. Recurrence of several structural elements in the observed structures suggests a "cut and paste" principle for the design and prediction of G-quadruplex topologies, for which different elements could be extracted from one G-quadruplex and inserted into another.
G4 notes
2 G-tetrads, 1 G4 helix, 1 G4 stem · 2(+LnD-Lw), basket(2+2), UUDD

Base-block schematics in six views [summary · tetrads · helices · stems · costacks · homepage]

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List of 2 G-tetrads [summary · schematics · helices · stems · costacks · homepage]

 1 glyco-bond=ss-- groove=-w-n planarity=0.256 type=other  nts=4 GGGG A.DG3,A.DG14,A.DG20,A.DG9
 2 glyco-bond=--ss groove=-w-n planarity=0.294 type=other  nts=4 GGGG A.DG4,A.DG15,A.DG19,A.DG8

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, 2 G-tetrad layers, INTRA-molecular, with 1 stem

 1  glyco-bond=ss-- groove=-w-n Major-->WC nts=4 GGGG A.DG3,A.DG14,A.DG20,A.DG9
 2  glyco-bond=--ss groove=-w-n WC-->Major nts=4 GGGG A.DG4,A.DG15,A.DG19,A.DG8
  step#1  mm(<>,outward)  area=11.47 rise=3.62 twist=19.1
  strand#1 DNA glyco-bond=s- nts=2 GG A.DG3,A.DG4
  strand#2 DNA glyco-bond=s- nts=2 GG A.DG14,A.DG15
  strand#3 DNA glyco-bond=-s nts=2 GG A.DG20,A.DG19
  strand#4 DNA glyco-bond=-s nts=2 GG A.DG9,A.DG8

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1 stacking diagram
 1  glyco-bond=ss-- groove=-w-n Major-->WC nts=4 GGGG A.DG3,A.DG14,A.DG20,A.DG9
2 glyco-bond=--ss groove=-w-n WC-->Major nts=4 GGGG A.DG4,A.DG15,A.DG19,A.DG8
step#1 mm(<>,outward) area=11.47 rise=3.62 twist=19.1

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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, 2 G-tetrad layers, 3 loops, INTRA-molecular, UUDD, anti-parallel, 2(+LnD-Lw), basket(2+2)

 1  glyco-bond=ss-- groove=-w-n Major-->WC nts=4 GGGG A.DG3,A.DG14,A.DG20,A.DG9
 2  glyco-bond=--ss groove=-w-n WC-->Major nts=4 GGGG A.DG4,A.DG15,A.DG19,A.DG8
  step#1  mm(<>,outward)  area=11.47 rise=3.62 twist=19.1
  strand#1  U DNA glyco-bond=s- nts=2 GG A.DG3,A.DG4
  strand#2  U DNA glyco-bond=s- nts=2 GG A.DG14,A.DG15
  strand#3  D DNA glyco-bond=-s nts=2 GG A.DG20,A.DG19
  strand#4  D DNA glyco-bond=-s nts=2 GG A.DG9,A.DG8
  loop#1 type=lateral   strands=[#1,#4] nts=3 GTA A.DG5,A.DT6,A.DA7
  loop#2 type=diagonal  strands=[#4,#2] nts=4 GTAG A.DG10,A.DT11,A.DA12,A.DG13
  loop#3 type=lateral   strands=[#2,#3] nts=3 TAg A.DT16,A.DA17,A.DI18

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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)