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

PDB-id
5mbr
Class
DNA
Method
NMR
Summary
Quadruplex with flipped tetrad formed by a human telomeric sequence
Reference
Dickerhoff, J., Haase, L., Langel, W., Weisz, K.: (2017) "Tracing Effects of Fluorine Substitutions on G-Quadruplex Conformational Changes." ACS Chem. Biol., 12, 1308-1315.
Abstract
A human telomere sequence that folds into an intramolecular (3 + 1)-hybrid G-quadruplex was modified by the incorporation of 2'-fluoro-2'-deoxyriboguanosines (FG) into syn positions of its outer tetrad. A circular dichroism and NMR spectral analysis reveals a nearly quantitative switch of the G-tetrad polarity with concerted syn↔anti transitions of all four G residues. These observations follow findings on a FG-substituted (3 + 1)-hybrid quadruplex with a different fold, suggesting a more general propensity of hybrid-type quadruplexes to undergo a tetrad polarity reversal. Two out of the three FG analogs in both modified quadruplexes adopt an S-type sugar pucker, challenging a sole contribution of N-type sugars in enforcing an anti glycosidic torsion angle associated with the tetrad flip. NMR restrained three-dimensional structures of the two substituted quadruplexes reveal a largely conserved overall fold but significant rearrangements of the overhang and loop nucleotides capping the flipped tetrad. Sugar pucker preferences of the FG analogs may be rationalized by different orientations of the fluorine atom and its resistance to be positioned within the narrow groove with its highly negative electrostatic potential and spine of water molecules.
G4 notes
3 G-tetrads, 1 G4 helix, 1 G4 stem · 3(-P-Lw-Ln), hybrid-1(3+1), UUDU

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=--s- groove=-wn- planarity=0.424 type=other  nts=4 ggGg A.GF2/3,A.GF2/9,A.DG17,A.GF2/21
 2 glyco-bond=--s- groove=-wn- planarity=0.273 type=other  nts=4 GGGG A.DG4,A.DG10,A.DG16,A.DG22
 3 glyco-bond=--s- groove=-wn- planarity=0.179 type=other  nts=4 GGGG A.DG5,A.DG11,A.DG15,A.DG23

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=--s- groove=-wn- WC-->Major nts=4 ggGg A.GF2/3,A.GF2/9,A.DG17,A.GF2/21
 2  glyco-bond=--s- groove=-wn- WC-->Major nts=4 GGGG A.DG4,A.DG10,A.DG16,A.DG22
 3  glyco-bond=--s- groove=-wn- WC-->Major nts=4 GGGG A.DG5,A.DG11,A.DG15,A.DG23
  step#1  pm(>>,forward)  area=16.09 rise=3.51 twist=23.6
  step#2  pm(>>,forward)  area=11.60 rise=3.48 twist=29.0
  strand#1 DNA glyco-bond=--- nts=3 gGG A.GF2/3,A.DG4,A.DG5
  strand#2 DNA glyco-bond=--- nts=3 gGG A.GF2/9,A.DG10,A.DG11
  strand#3 DNA glyco-bond=sss nts=3 GGG A.DG17,A.DG16,A.DG15
  strand#4 DNA glyco-bond=--- nts=3 gGG A.GF2/21,A.DG22,A.DG23

Download PDB file
Interactive view in 3Dmol.js

2 stacking diagrams
 1  glyco-bond=--s- groove=-wn- WC-->Major nts=4 ggGg A.GF2/3,A.GF2/9,A.DG17,A.GF2/21
2 glyco-bond=--s- groove=-wn- WC-->Major nts=4 GGGG A.DG4,A.DG10,A.DG16,A.DG22
step#1 pm(>>,forward) area=16.09 rise=3.51 twist=23.6

Download PDB file
Interactive view in 3Dmol.js

 2  glyco-bond=--s- groove=-wn- WC-->Major nts=4 GGGG A.DG4,A.DG10,A.DG16,A.DG22
3 glyco-bond=--s- groove=-wn- WC-->Major nts=4 GGGG A.DG5,A.DG11,A.DG15,A.DG23
step#2 pm(>>,forward) area=11.60 rise=3.48 twist=29.0

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, UUDU, anti-parallel, 3(-P-Lw-Ln), hybrid-1(3+1)

 1  glyco-bond=--s- groove=-wn- WC-->Major nts=4 ggGg A.GF2/3,A.GF2/9,A.DG17,A.GF2/21
 2  glyco-bond=--s- groove=-wn- WC-->Major nts=4 GGGG A.DG4,A.DG10,A.DG16,A.DG22
 3  glyco-bond=--s- groove=-wn- WC-->Major nts=4 GGGG A.DG5,A.DG11,A.DG15,A.DG23
  step#1  pm(>>,forward)  area=16.09 rise=3.51 twist=23.6
  step#2  pm(>>,forward)  area=11.60 rise=3.48 twist=29.0
  strand#1  U DNA glyco-bond=--- nts=3 gGG A.GF2/3,A.DG4,A.DG5
  strand#2  U DNA glyco-bond=--- nts=3 gGG A.GF2/9,A.DG10,A.DG11
  strand#3  D DNA glyco-bond=sss nts=3 GGG A.DG17,A.DG16,A.DG15
  strand#4  U DNA glyco-bond=--- nts=3 gGG A.GF2/21,A.DG22,A.DG23
  loop#1 type=propeller strands=[#1,#2] nts=3 TTA A.DT6,A.DT7,A.DA8
  loop#2 type=lateral   strands=[#2,#3] nts=3 TTA A.DT12,A.DT13,A.DA14
  loop#3 type=lateral   strands=[#3,#4] nts=3 TTA A.DT18,A.DT19,A.DA20

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)