2KAZ

Folding topology of a bimolecular DNA quadruplex containing a stable mini-hairpin motif within the connecting loop


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 6000 
  • Conformers Submitted: 
  • Selection Criteria: structures with acceptable covalent geometry 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Folding topology of a bimolecular DNA quadruplex containing a stable mini-hairpin motif within the diagonal loop

Balkwill, G.D.Garner, T.P.Williams, H.E.Searle, M.S.

(2009) J.Mol.Biol. 385: 1600-1615

  • DOI: 10.1016/j.jmb.2008.11.050

  • PubMed Abstract: 
  • We describe the NMR structural characterisation of a bimolecular anti-parallel DNA quadruplex d(G(3)ACGTAGTG(3))(2) containing an autonomously stable mini-hairpin motif inserted within the diagonal loop. A folding topology is identified that is diffe ...

    We describe the NMR structural characterisation of a bimolecular anti-parallel DNA quadruplex d(G(3)ACGTAGTG(3))(2) containing an autonomously stable mini-hairpin motif inserted within the diagonal loop. A folding topology is identified that is different from that observed for the analogous d(G(3)T(4)G(3))(2) dimer with the two structures differing in the relative orientation of the diagonal loops. This appears to reflect specific base stacking interactions at the quadruplex-duplex interface that are not present in the structure with the T(4)-loop sequence. A truncated version of the bimolecular quadruplex d(G(2)ACGTAGTG(2))(2), with only two core G-tetrads, is less stable and forms a heterogeneous mixture of three 2-fold symmetric quadruplexes with different loop arrangements. We demonstrate that the nature of the loop sequence, its ability to form autonomously stable structure, the relative stabilities of the hairpin loop and core quadruplex, and the ability to form favourable stacking interactions between these two motifs are important factors in controlling DNA G-quadruplex topology.


    Organizational Affiliation

    Centre for Biomolecular Sciences, School of Chemistry, University Park, Nottingham, UK.




Macromolecules

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Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*DGP*DGP*DGP*DAP*DCP*DGP*DTP*DAP*DGP*DTP*DGP*DGP*DG)-3'A,B13N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

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

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 6000 
  • Conformers Submitted: 
  • Selection Criteria: structures with acceptable covalent geometry 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-12-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance