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

PDB-id
2lk7
Class
DNA
Method
NMR
Summary
Monomer-dimer equilibrium for 5'-5' stacking of propeller-type parallel-stranded G-quadruplexes: NMR structural study
Reference
Do, N.Q., Phan, A.T.: (2012) "Monomer-Dimer Equilibrium for the 5'-5' Stacking of Propeller-Type Parallel-Stranded G-Quadruplexes: NMR Structural Study." Chemistry
Abstract
Guanine-rich sequence motifs, which contain tracts of three consecutive guanines connected by single non-guanine nucleotides, are abundant in the human genome and can form a robust G-quadruplex structure with high stability. Herein, by using NMR spectroscopy, we investigate the equilibrium between monomeric and 5'-5' stacked dimeric propeller-type G-quadruplexes that are formed by DNA sequences containing GGGT motifs. We show that the monomer-dimer equilibrium depends on a number of parameters, including the DNA concentration, DNA flanking sequences, the concentration and type of cations, and the temperature. We report on the high-definition structure of a simple monomeric G-quadruplex containing three single-residue loops, which could serve as a reference for propeller-type G-quadruplex structures in solution.
G4 notes
3 G-tetrads, 1 G4 helix, 1 G4 stem · 3(-P-P-P), parallel(4+0), UUUU

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=---- groove=---- planarity=0.086 type=planar nts=4 GGGG A.DG3,A.DG7,A.DG11,A.DG15
 2 glyco-bond=---- groove=---- planarity=0.096 type=planar nts=4 GGGG A.DG4,A.DG8,A.DG12,A.DG16
 3 glyco-bond=---- groove=---- planarity=0.117 type=planar nts=4 GGGG A.DG5,A.DG9,A.DG13,A.DG17

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, INTRA-molecular, with 1 stem

 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG7,A.DG11,A.DG15
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG8,A.DG12,A.DG16
 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG5,A.DG9,A.DG13,A.DG17
  step#1  pm(>>,forward)  area=12.32 rise=3.30 twist=29.7
  step#2  pm(>>,forward)  area=13.60 rise=3.49 twist=28.9
  strand#1 DNA glyco-bond=--- nts=3 GGG A.DG3,A.DG4,A.DG5
  strand#2 DNA glyco-bond=--- nts=3 GGG A.DG7,A.DG8,A.DG9
  strand#3 DNA glyco-bond=--- nts=3 GGG A.DG11,A.DG12,A.DG13
  strand#4 DNA glyco-bond=--- nts=3 GGG A.DG15,A.DG16,A.DG17

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2 stacking diagrams
 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG7,A.DG11,A.DG15
2 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG8,A.DG12,A.DG16
step#1 pm(>>,forward) area=12.32 rise=3.30 twist=29.7

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 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG8,A.DG12,A.DG16
3 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG5,A.DG9,A.DG13,A.DG17
step#2 pm(>>,forward) area=13.60 rise=3.49 twist=28.9

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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, 3 loops, INTRA-molecular, UUUU, parallel, 3(-P-P-P), parallel(4+0)

 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG7,A.DG11,A.DG15
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG8,A.DG12,A.DG16
 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG5,A.DG9,A.DG13,A.DG17
  step#1  pm(>>,forward)  area=12.32 rise=3.30 twist=29.7
  step#2  pm(>>,forward)  area=13.60 rise=3.49 twist=28.9
  strand#1  U DNA glyco-bond=--- nts=3 GGG A.DG3,A.DG4,A.DG5
  strand#2  U DNA glyco-bond=--- nts=3 GGG A.DG7,A.DG8,A.DG9
  strand#3  U DNA glyco-bond=--- nts=3 GGG A.DG11,A.DG12,A.DG13
  strand#4  U DNA glyco-bond=--- nts=3 GGG A.DG15,A.DG16,A.DG17
  loop#1 type=propeller strands=[#1,#2] nts=1 T A.DT6
  loop#2 type=propeller strands=[#2,#3] nts=1 T A.DT10
  loop#3 type=propeller strands=[#3,#4] nts=1 T A.DT14

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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)