5LIG

G-Quadruplex formed at the 5'-end of NHEIII_1 Element in human c-MYC promoter bound to triangulenium based fluorescence probe DAOTA-M2

• PDB DOI: https://doi.org/10.2210/pdb5LIG/pdb
• NAKB: 5LIG
• BMRB: 34025

• Classification: DNA
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2016-07-14 Released: 2016-09-14 
• Deposition Author(s): Kotar, A., Wang, B., Shivalingam, A., Gonzalez-Garcia, J., Vilar, R., Plavec, J.
• Funding Organization(s): Slovenian Research Agency

---

Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 10 
• Selection Criteria: structures with the least restraint violations 

Literature

NMR Structure of a Triangulenium-Based Long-Lived Fluorescence Probe Bound to a G-Quadruplex.

Kotar, A., Wang, B., Shivalingam, A., Gonzalez-Garcia, J., Vilar, R., Plavec, J.

(2016) Angew Chem Int Ed Engl 55: 12508-12511

• PubMed: 27577037 
• DOI: https://doi.org/10.1002/anie.201606877
• Primary Citation of Related Structures:  
  5LIG


• PubMed Abstract: 
  

  An NMR structural study of the interaction between a small-molecule optical probe (DAOTA-M2) and a G-quadruplex from the promoter region of the c-myc oncogene revealed that they interact at 1:2 binding stoichiometry. NMR-restrained structural calculations show that binding of DAOTA-M2 occurs mainly through π-π stacking between the polyaromatic core of the ligand and guanine residues of the outer G-quartets. Interestingly, the binding affinities of DAOTA-M2 differ by a factor of two for the outer G-quartets of the unimolecular parallel G-quadruplex under study. Unrestrained MD calculations indicate that DAOTA-M2 displays significant dynamic behavior when stacked on a G-quartet plane. These studies provide molecular guidelines for the design of triangulenium derivatives that can be used as optical probes for G-quadruplexes.

---

Organizational Affiliation: 

Slovenian NMR Center, National Institute of Chemistry, Hajdrihova 19, 1000, Ljubljana, Slovenia.

Biological Assembly 1  

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 7.09 kDa 
• Atom Count: 481 
• Modelled Residue Count: 19 
• Deposited Residue Count: 19 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*AP*GP*GP*GP*AP*GP*GP*GP*TP*AP*GP*GP*GP*AP*GP*GP*GP*T)-3')	A	19	Homo sapiens

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
6XM	B [auth A], C [auth A]	8,12-bis(2-morpholinoethyl)-8H-benzo[ij]xantheno[1,9,8-cdef][2,7]naphthyridin-12-iumhexafluorophosphate C31 H34 N4 O3 JDODSALIMITEDK-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 10 
• Selection Criteria: structures with the least restraint violations 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-09-14 
Deposition Author(s): Kotar, A., Wang, B., Shivalingam, A., Gonzalez-Garcia, J., Vilar, R., Plavec, J.

---

Funding Organization	Location	Grant Number
Slovenian Research Agency	Slovenia	P1-242
Slovenian Research Agency	Slovenia	J1-6733

Revision History  

• Version 1.0: 2016-09-14
  Type: Initial release
  
• Version 1.1: 2016-09-28
  Changes: Database references
• Version 1.2: 2018-02-14
  Changes: Data collection
• Version 2.0: 2018-03-07
  Changes: Advisory, Atomic model, Derived calculations, Non-polymer description
• Version 2.1: 2019-05-08
  Changes: Data collection