2N60

G-quadruplexes with (4n-1) guanines in the G-tetrad core: formation of a G-triad water complex and implication for small-molecule binding


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 10000 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

G-quadruplexes with (4n - 1) guanines in the G-tetrad core: formation of a G-triadwater complex and implication for small-molecule binding

Heddi, B.Martin-Pintado, N.Serimbetov, Z.Kari, T.M.Phan, A.T.

(2016) Nucleic Acids Res. 44: 910-916

  • DOI: 10.1093/nar/gkv1357

  • PubMed Abstract: 
  • G-quadruplexes are non-canonical structures of nucleic acids, in which guanine bases form planar G-tetrads (G·G·G·G) that stack on each other in the core of the structure. G-quadruplexes generally contain multiple times of four (4n) guanines in the c ...

    G-quadruplexes are non-canonical structures of nucleic acids, in which guanine bases form planar G-tetrads (G·G·G·G) that stack on each other in the core of the structure. G-quadruplexes generally contain multiple times of four (4n) guanines in the core. Here, we study the structure of G-quadruplexes with only (4n - 1) guanines in the core. The solution structure of a DNA sequence containing 11 guanines showed the formation of a parallel G-quadruplex involving two G-tetrads and one G-triad with a vacant site. Molecular dynamics simulation established the formation of a stable G-triad·water complex, where water molecules mimic the position of the missing guanine in the vacant site. The concept of forming G-quadruplexes with missing guanines in the core broadens the current definition of G-quadruplex-forming sequences. The potential ability of such structures to bind different metabolites, including guanine, guanosine and GTP, in the vacant site, could have biological implications in regulatory functions. Formation of this unique binding pocket in the G-triad could be used as a specific target in drug design.


    Organizational Affiliation

    School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore.,School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore heddibrahim@ntu.edu.sg.,School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore phantuan@ntu.edu.sg.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*TP*TP*GP*TP*GP*TP*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*T)-3')A18synthetic construct
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 10000 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-06-01
    Type: Initial release