1C35

SOLUTION STRUCTURE OF A QUADRUPLEX FORMING DNA AND ITS INTERMIDIATE


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Submitted: 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structures of the potassium-saturated, 2:1, and intermediate, 1:1, forms of a quadruplex DNA.

Marathias, V.M.Bolton, P.H.

(2000) Nucleic Acids Res 28: 1969-1977

  • DOI: 10.1093/nar/28.9.1969
  • Primary Citation of Related Structures:  
    1C38, 1C35, 1C34, 1C32

  • PubMed Abstract: 
  • Potassium can stabilize the formation of chair- or edge-type quadruplex DNA structures and appears to be the only naturally occurring cation that can do so. As quadruplex DNAs may be important in the structure of telomere, centromere, triplet repeat ...

    Potassium can stabilize the formation of chair- or edge-type quadruplex DNA structures and appears to be the only naturally occurring cation that can do so. As quadruplex DNAs may be important in the structure of telomere, centromere, triplet repeat and other DNAs, information about the details of the potassium-quadruplex DNA interactions are of interest. The structures of the 1:1 and the fully saturated, 2:1, potassium-DNA complexes of d(GGTTGGTGTGGTTGG) have been determined using the combination of experimental NMR results and restrained molecular dynamics simulations. The refined structures have been used to model the interactions at the potassium binding sites. Comparison of the 1:1 and 2:1 potassium:DNA structures indicates how potassium binding can determine the folding pattern of the DNA. In each binding site potassium interacts with the carbonyl oxygens of both the loop thymine residues and the guanine residues of the adjacent quartet.


    Related Citations: 
    • Determination of the Number and Location of the Manganese Binding Sites of DNA Quadruplexes in Solution by EPR and NMR in the Presence and Absence of Thrombin
      Bolton, P.H., Marathias, V.M., Wang, K.
      (1996) J Mol Biol 260: 378

    Organizational Affiliation

    Chemistry Department, Wesleyan University, Middletown, CT 06459, USA.



Macromolecules
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*GP*GP*TP*TP*GP*GP*TP*GP*TP*GP*GP*TP*TP*GP*G)-3')A15N/A
    Small Molecules
    Ligands 1 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    K
    Query on K

    Download CCD File 
    A
    POTASSIUM ION
    K
    NPYPAHLBTDXSSS-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: SOLUTION NMR
    • Conformers Submitted: 
    • OLDERADO: 1C35 Olderado

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    Revision History 

    • Version 1.0: 1999-08-18
      Type: Initial release
    • Version 1.1: 2008-04-27
      Changes: Version format compliance
    • Version 1.2: 2011-07-13
      Changes: Version format compliance