6YEP

LNA modified G-quadruplex with flipped G-tract and central tetrad

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

  • Deposited: 2020-03-25 Released: 2020-09-02 
  • Deposition Author(s): Weisz, K., Haase, L.
  • Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 14 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Locked nucleic acid building blocks as versatile tools for advanced G-quadruplex design.

Haase, L.Weisz, K.

(2020) Nucleic Acids Res 48: 10555-10566

  • DOI: https://doi.org/10.1093/nar/gkaa720
  • Primary Citation of Related Structures:  
    6YCV, 6YEP

  • PubMed Abstract: 

    A hybrid-type G-quadruplex is modified with LNA (locked nucleic acid) and 2'-F-riboguanosine in various combinations at the two syn positions of its third antiparallel G-tract. LNA substitution in the central tetrad causes a complete rearrangement to either a V-loop or antiparallel structure, depending on further modifications at the 5'-neighboring site. In the two distinct structural contexts, LNA-induced stabilization is most effective compared to modifications with other G surrogates, highlighting a potential use of LNA residues for designing not only parallel but various more complex G4 structures. For instance, the conventional V-loop is a structural element strongly favored by an LNA modification at the V-loop 3'-end in contrast with an alternative V-loop, clearly distinguishable by altered conformational properties and base-backbone interactions as shown in a detailed analysis of V-loop structures.


  • Organizational Affiliation

    Institut für Biochemie, Universität Greifswald, Felix-Hausdorff-Str. 4, D-17489 Greifswald, Germany.


Macromolecules

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains LengthOrganismImage
DNA (5'-D(*GP*GP*GP*AP*TP*GP*GP*GP*AP*CP*AP*CP*AP*G)-R(P*(LCG))-D(P*GP*GP*AP*CP*GP*GP*G)-3')22synthetic construct
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 14 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the lowest energy 

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  (Full details and data files)

  • Version 1.0: 2020-09-02
    Type: Initial release
  • Version 1.1: 2020-09-16
    Changes: Database references
  • Version 1.2: 2020-10-21
    Changes: Database references
  • Version 1.3: 2024-05-15
    Changes: Data collection, Database references