2LYG

Fuc_TBA


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 12 
  • Conformers Submitted: 12 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Carbohydrate-DNA interactions at G-quadruplexes: folding and stability changes by attaching sugars at the 5'-end.

Gomez-Pinto, I.Vengut-Climent, E.Lucas, R.Avino, A.Eritja, R.Gonzalez, C.Morales, J.C.

(2013) Chemistry 19: 1920-1927

  • DOI: 10.1002/chem.201203902

  • PubMed Abstract: 
  • Quadruplex DNA structures are attracting an enormous interest in many areas of chemistry, ranging from chemical biology, supramolecular chemistry to nanoscience. We have prepared carbohydrate-DNA conjugates containing the oligonucleotide sequences of ...

    Quadruplex DNA structures are attracting an enormous interest in many areas of chemistry, ranging from chemical biology, supramolecular chemistry to nanoscience. We have prepared carbohydrate-DNA conjugates containing the oligonucleotide sequences of G-quadruplexes (thrombin binding aptamer (TBA) and human telomere (TEL)), measured their thermal stability and studied their structure in solution by using NMR and molecular dynamics. The solution structure of a fucose-TBA conjugate shows stacking interactions between the carbohydrate and the DNA G-tetrad in addition to hydrogen bonding and hydrophobic contacts. We have also shown that attaching carbohydrates at the 5'-end of a quadruplex telomeric sequence can alter its folding topology. These results suggest the possibility of modulating the folding of the G-quadruplex by linking carbohydrates and have clear implications in molecular recognition and the design of new G-quadruplex ligands.


    Organizational Affiliation

    Instituto de Química Física Rocasolano, CSIC, Serrano 119, 28006 Madrid, Spain.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(P*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
1CF
Query on 1CF

Download SDF File 
Download CCD File 
A
2-hydroxyethyl 6-deoxy-beta-L-galactopyranoside
C8 H16 O6
WEKZOSZDHREWIU-SHGPDSBTSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 12 
  • Conformers Submitted: 12 
  • 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: 2014-01-29
    Type: Initial release
  • Version 1.1: 2014-03-19
    Type: Database references