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

PDB-id
2mb2
Class
DNA
Method
NMR
Summary
Parallel-stranded G-quadruplex in DNA poly-g stretches
Reference
Sengar, A., Heddi, B., Phan, A.T.: (2014) "Formation of g-quadruplexes in poly-g sequences: structure of a propeller-type parallel-stranded g-quadruplex formed by a g15 stretch." Biochemistry, 53, 7718-7723.
Abstract
Poly-G sequences are found in different genomes including human and have the potential to form higher-order structures with various applications. Previously, long poly-G sequences were thought to lead to multiple possible ways of G-quadruplex folding, rendering their structural characterization challenging. Here we investigate the structure of G-quadruplexes formed by poly-G sequences d(TTG(n)T), where n = 12 to 19. Our data show the presence of multiple and/or higher-order G-quadruplex structures in most sequences. Strikingly, NMR spectra of the TTG₁₅T sequence containing a stretch of 15 continuous guanines are exceptionally well-resolved and indicate the formation of a well-defined G-quadruplex structure. The NMR solution structure of this sequence revealed a propeller-type parallel-stranded G-quadruplex containing three G-tetrad layers and three single-guanine propeller loops. The same structure can potentially form anywhere along a long G(n) stretch, making it unique for molecular recognition by other cellular molecules.
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=0.102 type=planar nts=4 GGGG A.DG3,A.DG7,A.DG11,A.DG15
 2 glyco-bond=---- groove=---- planarity=0.083 type=planar nts=4 GGGG A.DG4,A.DG8,A.DG12,A.DG16
 3 glyco-bond=---- groove=---- planarity=0.158 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=9.93  rise=3.32 twist=31.9
  step#2  pm(>>,forward)  area=13.25 rise=3.41 twist=31.5
  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

Download PDB file
Interactive view in 3Dmol.js

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=9.93 rise=3.32 twist=31.9

Download PDB file
Interactive view in 3Dmol.js

 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=13.25 rise=3.41 twist=31.5

Download PDB file
Interactive view in 3Dmol.js

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=9.93  rise=3.32 twist=31.9
  step#2  pm(>>,forward)  area=13.25 rise=3.41 twist=31.5
  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 G A.DG6
  loop#2 type=propeller strands=[#2,#3] nts=1 G A.DG10
  loop#3 type=propeller strands=[#3,#4] nts=1 G A.DG14

Download PDB file
Interactive view in 3Dmol.js

List of 0 G4 coaxial stacks [summary · schematics · tetrads · helices · stems · homepage]

List of 0 non-stem G4-loops (including the two closing Gs)