8C7A

Slow cation movements within tetramolecular G-quadruplex: vacant cation binding sites in addition to all syn G-quartet


Experimental Data Snapshot

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

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Insight into Tetramolecular DNA G-Quadruplexes Associated with ALS and FTLD: Cation Interactions and Formation of Higher-Ordered Structure.

Zalar, M.Wang, B.Plavec, J.Sket, P.

(2023) Int J Mol Sci 24

  • DOI: https://doi.org/10.3390/ijms241713437
  • Primary Citation of Related Structures:  
    8C7A, 8C7B

  • PubMed Abstract: 

    The G 4 C 2 hexanucleotide repeat expansion in the c9orf72 gene is a major genetic cause of familial amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD), with the formation of G-quadruplexes directly linked to the development of these diseases. Cations play a crucial role in the formation and structure of G-quadruplexes. In this study, we investigated the impact of biologically relevant potassium ions on G-quadruplex structures and utilized 15 N-labeled ammonium cations as a substitute for K + ions to gain further insights into cation binding and exchange dynamics. Through nuclear magnetic resonance spectroscopy and molecular dynamics simulations, we demonstrate that the single d(G 4 C 2 ) repeat, in the presence of 15 NH 4 + ions, adopts a tetramolecular G-quadruplex with an all- syn quartet at the 5'-end. The movement of 15 NH 4 + ions through the central channel of the G-quadruplex, as well as to the bulk solution, is governed by the vacant cation binding site, in addition to the all- syn quartet at the 5'-end. Furthermore, the addition of K + ions to G-quadruplexes folded in the presence of 15 NH 4 + ions induces stacking of G-quadruplexes via their 5'-end G-quartets, leading to the formation of stable higher-ordered species.


  • Organizational Affiliation

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


Macromolecules

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains LengthOrganismImage
DNA (5'-D(*GP*GP*GP*GP*CP*C)-3')
A, B, C, D
6Homo sapiens
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

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

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Slovenian Research AgencySloveniaP1-0242
Slovenian Research AgencySloveniaJ1-7108
Slovenian Research AgencySloveniaJ1-6733
Slovenian Research AgencySloveniaJ1-1704
Slovenian Research AgencySloveniaJ3-1759
Slovenian Research AgencySloveniaJ7-9399

Revision History  (Full details and data files)

  • Version 1.0: 2023-11-22
    Type: Initial release