6YCV

2'-F-riboguanosine and LNA modified hybrid type G-quadruplex with V-loop

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

  • Deposited: 2020-03-19 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: 10 
  • Conformers Submitted: 10 
  • Selection Criteria: all calculated structures submitted 

wwPDB Validation   3D Report Full Report


This is version 1.2 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

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Entity ID: 1
MoleculeChains LengthOrganismImage
DNA (5'-D(*GP*GP*GP*AP*TP*GP*GP*GP*AP*CP*AP*CP*AP*(GF2))-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: 10 
  • Conformers Submitted: 10 
  • Selection Criteria: all calculated structures submitted 

Structure Validation

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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