6KFI

NMR solution structure of the 1:1 complex of Tel26 G-quadruplex and a tripodal cationic fluorescent probe NBTE


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 15 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Quantitative Detection of G-Quadruplex DNA in Live Cells Based on Photon Counts and Complex Structure Discrimination.

Liu, L.Y.Liu, W.Wang, K.N.Zhu, B.C.Xia, X.Y.Ji, L.N.Mao, Z.W.

(2020) Angew Chem Int Ed Engl 59: 9719-9726

  • DOI: https://doi.org/10.1002/anie.202002422
  • Primary Citation of Related Structures:  
    6KFI, 6KFJ

  • PubMed 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 (Φ f ) enhancement upon G-quadruplex binding. We determined two NBTE-G-quadruplex complex structures with high Φ f 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 Φ f 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.


  • Organizational Affiliation

    MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, P. R. China.


Macromolecules
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains LengthOrganismImage
G-quadruplex DNA (26-MER)26Homo sapiens
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
D6F (Subject of Investigation/LOI)
Query on D6F

Download Ideal Coordinates CCD File 
B [auth A]4,4',4''-(nitrilotris(benzene-4,1-diyl))tris(1-ethylpyridin-1-ium) iodide
C39 H39 N4
GYPMVNLFLRHFFL-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 15 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-08
    Type: Initial release
  • Version 1.1: 2020-09-23
    Changes: Database references
  • Version 1.2: 2024-05-01
    Changes: Data collection, Database references