8JIH | pdb_00008jih

human telomere two-quartet G-quadruplex at pH 5.0

• PDB DOI: https://doi.org/10.2210/pdb8JIH/pdb
• NAKB: 8JIH

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


• Deposited: 2023-05-26 Released: 2024-04-03 
• Deposition Author(s): Wang, B., Galer, P., 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

Unveiling the structural mechanism of a G-quadruplex pH-Driven switch.

Galer, P., Wang, B., Plavec, J., Sket, P.

(2023) Biochimie 214: 73-82

• PubMed: 37573019 
• DOI: https://doi.org/10.1016/j.biochi.2023.08.002
• Primary Citation Related Structures: 
  8JIC, 8JIH


• PubMed Abstract: 
  

  The human telomere oligonucleotide, d[TAGGG(TTAGGG) ₂ TTAGG] (TAGGG), can adopt two distinct 2-G-quartet G-quadruplex structures at pH 7.0 and 5.0, referred to as the TD and KDH ⁺ forms, respectively. By using a combination of NMR and computational techniques, we determined high-resolution structures of both forms, which revealed unique loop architectures, base triples, and base pairs that play a crucial role in the pH-driven structural transformation of TAGGG. Our study demonstrated that TAGGG represents a reversible pH-driven switch system where the stability and pH-induced structural transformation of the G-quadruplexes are influenced by the terminal residues and base triples. Gaining insight into the factors that regulate the formation of G-quadruplexes and their pH-sensitive structural equilibrium holds great potential for the rational design of novel DNA based pH-driven switches. These advancements in understanding create exciting opportunities for applications in the field of nanotechnology, specifically in the development of bio-nano-motors.

---

Organizational Affiliation: 
• Slovenian NMR Center, National Institute of Chemistry, Hajdrihova 19, SI-1000, Ljubljana, Slovenia.
Slovenian NMR Center, National Institute of Chemistry, Hajdrihova 19, SI-1000, Ljubljana, Slovenia; EN-FIST Center of Excellence, SI-1000, Ljubljana, Slovenia; Faculty of Chemistry and Chemical Technology, University of Ljubljana, SI-1000, Ljubljana, Slovenia.
Slovenian NMR Center, National Institute of Chemistry, Hajdrihova 19, SI-1000, Ljubljana, Slovenia. Electronic address: [e-mail].

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: NMR Distance Restraints

Macromolecule Content 

• Total Structure Weight: 6.96 kDa 
• Atom Count: 463 
• Modeled Residue Count: 22 
• Deposited Residue Count: 22 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*G)-3')	A	22	Homo sapiens

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: 2024-04-03 
Deposition Author(s): Wang, B., Galer, P., Plavec, J.

---

Funding Organization	Location	Grant Number
Slovenian Research Agency	Slovenia	P1-0242
Slovenian Research Agency	Slovenia	J1-1704
Slovenian Research Agency	Slovenia	J1-7108

Revision History  

• Version 1.0: 2024-04-03
  Type: Initial release
  
• Version 1.1: 2024-05-08
  Changes: Database references