2MCC

Structural studies on dinuclear ruthenium(II) complexes that bind diastereoselectively to an anti-parallel folded human telomere sequence


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 20 
  • Conformers Submitted: 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structural Studies on Dinuclear Ruthenium(II) Complexes That Bind Diastereoselectively to an Antiparallel Folded Human Telomere Sequence.

Wilson, T.Costa, P.J.Felix, V.Williamson, M.P.Thomas, J.A.

(2013) J Med Chem 56: 8674-8683

  • DOI: https://doi.org/10.1021/jm401119b
  • Primary Citation of Related Structures:  
    2MCC, 2MCO

  • PubMed Abstract: 

    We report DNA binding studies of the dinuclear ruthenium ligand [{Ru(phen)2}2tpphz](4+) in enantiomerically pure forms. As expected from previous studies of related complexes, both isomers bind with similar affinity to B-DNA and have enhanced luminescence. However, when tested against the G-quadruplex from human telomeres (which we show to form an antiparallel basket structure with a diagonal loop across one end), the ΛΛ isomer binds approximately 40 times more tightly than the ΔΔ, with a stronger luminescence. NMR studies show that the complex binds at both ends of the quadruplex. Modeling studies, based on experimentally derived restraints obtained for the closely related [{Ru(bipy)2}2tpphz](4+), show that the ΛΛ isomer fits neatly under the diagonal loop, whereas the ΔΔ isomer is unable to bind here and binds at the lateral loop end. Molecular dynamics simulations show that the ΔΔ isomer is prevented from binding under the diagonal loop by the rigidity of the loop. We thus present a novel enantioselective binding substrate for antiparallel basket G-quadruplexes, with features that make it a useful tool for quadruplex studies.


  • Organizational Affiliation

    Department of Chemistry, University of Sheffield , Dainton Building, Brook Hill, Sheffield S3 7HF, U.K.


Macromolecules

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains LengthOrganismImage
human_telomere_quadruplex22N/A
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
RUL
Query on RUL

Download Ideal Coordinates CCD File 
B [auth A]tetrakis(2,2'-bipyridine-kappa~2~N~1~,N~1'~)(mu-tetrapyrido[3,2-a:2',3'-c:3'',2''-h:2''',3'''-j]phenazine-1kappa~2~N~4~,N~5~:2kappa~2~N~13~,N~14~)diruthenium(4+)
C64 H44 N14 Ru2
CUPZTUKKQZECGK-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 20 
  • Conformers Submitted: 
  • 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: 2013-10-02
    Type: Initial release
  • Version 1.1: 2013-10-16
    Changes: Database references
  • Version 1.2: 2014-01-22
    Changes: Database references
  • Version 1.3: 2023-06-14
    Changes: Data collection, Database references, Derived calculations, Other
  • Version 1.4: 2024-05-15
    Changes: Data collection, Database references