Summary information

PDB id
6kfi
Class
DNA
Method
NMR
Summary
NMR solution structure of the 1:1 complex of tel26 g-quadruplex and a tripodal cationic fluorescent probe nbte
Reference
Liu LY, Liu W, Wang KN, Zhu BC, Xia XY, Ji LN, Mao ZW (2020): "Quantitative Detection of G-Quadruplex DNA in Live Cells Based on Photon Counts and Complex Structure Discrimination." Angew.Chem.Int.Ed.Engl., 59, 9719-9726. doi: 10.1002/anie.202002422.
Abstract
G-quadruplex DNA show structural polymorphism, leading to challenges in the use of selective recognition probes for the accurate detection of G-quadruplexes in vivo. Herein, we present a tripodal cationic fluorescent probe, NBTE, which showed distinguishable fluorescence lifetime responses between G-quadruplexes and other DNA topologies, and fluorescence quantum yield (Φf ) enhancement upon G-quadruplex binding. We determined two NBTE-G-quadruplex complex structures with high Φf values by NMR spectroscopy. The structures indicated NBTE interacted with G-quadruplexes using three arms through π-π stacking, differing from that with duplex DNA using two arms, which rationalized the higher Φf values and lifetime response of NBTE upon G-quadruplex binding. Based on photon counts of FLIM, we detected the percentage of G-quadruplex DNA in live cells with NBTE and found G-quadruplex DNA content in cancer cells is 4-fold that in normal cells, suggesting the potential applications of this probe in cancer cell detection.
G4 notes
3 G-tetrads, 1 G4 helix, 1 G4 stem, 3(+P+Lw+Ln), (3+1), UUDU

Base-block schematics in six views

PyMOL session file PDB file View in 3Dmol.js

List of 3 G-tetrads

 1 glyco-bond=.s-s groove=.nw. planarity=0.234 type=other  nts=4 GGGG A.DG4,A.DG22,A.DG18,A.DG10
 2 glyco-bond=--s- groove=-wn- planarity=0.285 type=other  nts=4 GGGG A.DG5,A.DG11,A.DG17,A.DG23
 3 glyco-bond=--s- groove=-wn- planarity=0.326 type=other  nts=4 GGGG A.DG6,A.DG12,A.DG16,A.DG24

List of 1 G4-helix

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-s groove=.nw. WC-->Major nts=4 GGGG A.DG4,A.DG22,A.DG18,A.DG10
 2  glyco-bond=--s- groove=-nw- Major-->WC nts=4 GGGG A.DG5,A.DG23,A.DG17,A.DG11
 3  glyco-bond=--s- groove=-nw- Major-->WC nts=4 GGGG A.DG6,A.DG24,A.DG16,A.DG12
  step#1  mm(<>,outward)  area=12.67 rise=4.09 twist=19.4
  step#2  pm(>>,forward)  area=13.52 rise=3.81 twist=27.2
  strand#1 DNA glyco-bond=.-- nts=3 GGG A.DG4,A.DG5,A.DG6
  strand#2 DNA glyco-bond=s-- nts=3 GGG A.DG22,A.DG23,A.DG24
  strand#3 DNA glyco-bond=-ss nts=3 GGG A.DG18,A.DG17,A.DG16
  strand#4 DNA glyco-bond=s-- nts=3 GGG A.DG10,A.DG11,A.DG12

Download PDB file
Interactive view in 3Dmol.js

2 stacking diagrams
 1  glyco-bond=.s-s groove=.nw. WC-->Major nts=4 GGGG A.DG4,A.DG22,A.DG18,A.DG10
2 glyco-bond=--s- groove=-nw- Major-->WC nts=4 GGGG A.DG5,A.DG23,A.DG17,A.DG11
step#1 mm(<>,outward) area=12.67 rise=4.09 twist=19.4

Download PDB file
Interactive view in 3Dmol.js

 2  glyco-bond=--s- groove=-nw- Major-->WC nts=4 GGGG A.DG5,A.DG23,A.DG17,A.DG11
3 glyco-bond=--s- groove=-nw- Major-->WC nts=4 GGGG A.DG6,A.DG24,A.DG16,A.DG12
step#2 pm(>>,forward) area=13.52 rise=3.81 twist=27.2

Download PDB file
Interactive view in 3Dmol.js

List of 1 G4-stem

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, hybrid-(mixed), 3(+P+Lw+Ln), (3+1)

 1  glyco-bond=.s-s groove=.nw. WC-->Major nts=4 GGGG A.DG4,A.DG22,A.DG18,A.DG10
 2  glyco-bond=--s- groove=-nw- Major-->WC nts=4 GGGG A.DG5,A.DG23,A.DG17,A.DG11
 3  glyco-bond=--s- groove=-nw- Major-->WC nts=4 GGGG A.DG6,A.DG24,A.DG16,A.DG12
  step#1  mm(<>,outward)  area=12.67 rise=4.09 twist=19.4
  step#2  pm(>>,forward)  area=13.52 rise=3.81 twist=27.2
  strand#1  U DNA glyco-bond=.-- nts=3 GGG A.DG4,A.DG5,A.DG6
  strand#2  U DNA glyco-bond=s-- nts=3 GGG A.DG22,A.DG23,A.DG24
  strand#3  D DNA glyco-bond=-ss nts=3 GGG A.DG18,A.DG17,A.DG16
  strand#4  U DNA glyco-bond=s-- nts=3 GGG A.DG10,A.DG11,A.DG12
  loop#1 type=propeller strands=[#1,#4] nts=3 TTA A.DT7,A.DT8,A.DA9
  loop#2 type=lateral   strands=[#4,#3] nts=3 TTA A.DT13,A.DT14,A.DA15
  loop#3 type=lateral   strands=[#3,#2] nts=3 TTA A.DT19,A.DT20,A.DA21

Download PDB file
Interactive view in 3Dmol.js