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 1.3 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:  
    1C32, 1C34, 1C35, 1C38

  • 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 and other DNAs, information about the details of the potassium-quadruplex DNA interactions are of interest ...

    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   |   3D 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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A],
D [auth A],
E [auth A],
F [auth A],
B [auth A],
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
S [auth A],
T [auth A],
U [auth A]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Submitted: 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 1.3: 2022-02-16
    Changes: Database references, Derived calculations