2MWZ

Xanthine and 8-oxoguanine in G-quadruplexes: formation of a G G X O tetrad


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Xanthine and 8-oxoguanine in G-quadruplexes: formation of a GGXO tetrad.

Cheong, V.V.Heddi, B.Lech, C.J.Phan, A.T.

(2015) Nucleic Acids Res. 43: 10506-10514

  • DOI: 10.1093/nar/gkv826

  • PubMed Abstract: 
  • G-quadruplexes are four-stranded structures built from stacked G-tetrads (G·G·G·G), which are planar cyclical assemblies of four guanine bases interacting through Hoogsteen hydrogen bonds. A G-quadruplex containing a single guanine analog substitutio ...

    G-quadruplexes are four-stranded structures built from stacked G-tetrads (G·G·G·G), which are planar cyclical assemblies of four guanine bases interacting through Hoogsteen hydrogen bonds. A G-quadruplex containing a single guanine analog substitution, such as 8-oxoguanine (O) or xanthine (X), would suffer from a loss of a Hoogsteen hydrogen bond within a G-tetrad and/or potential steric hindrance. We show that a proper arrangement of O and X bases can reestablish the hydrogen-bond pattern within a G·G·X·O tetrad. Rational incorporation of G·G·X·O tetrads in a (3+1) G-quadruplex demonstrated a similar folding topology and thermal stability to that of the unmodified G-quadruplex. pH titration conducted on X·O-modified G-quadruplexes indicated a protonation-deprotonation equilibrium of X with a pKa ∼6.7. The solution structure of a G-quadruplex containing a G·G·X·O tetrad was determined, displaying the same folding topology in both the protonated and deprotonated states. A G-quadruplex containing a deprotonated X·O pair was shown to exhibit a more electronegative groove compared to that of the unmodified one. These differences are likely to manifest in the electronic properties of G-quadruplexes and may have important implications for drug targeting and DNA-protein interactions.


    Organizational Affiliation

    School of Physical and Mathematical Sciences, Nanyang Technological University, 637371 Singapore.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*TP*TP*GP*GP*GP*TP*TP*AP*(8OG)P*GP*GP*TP*TP*AP*GP*GP*(3ZO)P*TP*TP*AP*GP*GP*GP*A)-3')A24N/A
Small Molecules
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
3ZO
Query on 3ZO
A
DNA LINKINGC10 H13 N4 O8 P

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8OG
Query on 8OG
A
DNA LINKINGC10 H14 N5 O8 PDG
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • 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: 2015-10-14
    Type: Initial release
  • Version 1.1: 2015-12-23
    Type: Database references
  • Version 1.2: 2016-07-06
    Type: Structure summary