6ZTE

Structure of a parallel c-myc modified with 5' duplex stem-loop and 3' diagonal snap-back loop

  • Classification: DNA
  • Organism(s): synthetic construct
  • Mutation(s): No 

  • Deposited: 2020-07-20 Released: 2020-10-07 
  • Deposition Author(s): Vianney, Y.M., Weisz, K.
  • Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 10 
  • Conformers Submitted: 10 
  • Selection Criteria: all calculated structures submitted 

wwPDB Validation 3D Report Full Report



Literature

Quadruplex-Duplex Junction: A High-Affinity Binding Site for Indoloquinoline Ligands.

Vianney, Y.M.Preckwinkel, P.Mohr, S.Weisz, K.

(2020) Chemistry 

  • DOI: 10.1002/chem.202003540
  • Primary Citation of Related Structures:  
    6ZTE, 6ZL9, 6ZL2

  • PubMed Abstract: 
  • A parallel quadruplex derived from the Myc promoter sequence was extended by a stem-loop duplex at either its 5'- or 3'-terminus to mimic a quadruplex-duplex (Q-D) junction as a potential genomic target. High-resolution structures of the hybrids demo ...

    A parallel quadruplex derived from the Myc promoter sequence was extended by a stem-loop duplex at either its 5'- or 3'-terminus to mimic a quadruplex-duplex (Q-D) junction as a potential genomic target. High-resolution structures of the hybrids demonstrate continuous stacking of the duplex on the quadruplex core without significant perturbations. An indoloquinoline ligand carrying an aminoalkyl sidechain was shown to bind the Q-D hybrids with a very high affinity in the order K a ~ 10 7 M -1 irrespective of the duplex location at the quadruplex 3'- or 5'-end. NMR chemical shift perturbations identified the tetrad face of the Q-D junction as specific binding site for the ligand. However, calorimetric analyses revealed significant differences in the thermodynamic profiles upon binding to hybrids with either a duplex extension at the quadruplex 3'- or 5'-terminus. A large enthalpic gain and considerable hydrophobic effects are accompanied by the binding of one ligand to the 3'-Q-D junction, whereas non-hydrophobic entropic contributions favor binding with formation of a 2:1 ligand-quadruplex complex in case of the 5'-Q-D hybrid.


    Organizational Affiliation

    Universität Greifswald, Institut für Biochemie, Felix-Hausdorff-Str. 4, 17487, Greifswald, GERMANY.



Macromolecules
Find similar nucleic acids by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsLengthOrganismImage
DNA (36-MER)A36synthetic construct
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 10 
  • Conformers Submitted: 10 
  • Selection Criteria: all calculated structures submitted 
  • OLDERADO: 6ZTE Olderado

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanyWE 1933/15-1

Revision History 

  • Version 1.0: 2020-10-07
    Type: Initial release