6RS3

2'-F-riboguanosine modified G-quadruplex with V-loop


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 20 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Sugar Puckering Drives G-Quadruplex Refolding: Implications for V-Shaped Loops.

Haase, L.Dickerhoff, J.Weisz, K.

(2019) Chemistry --: --

  • DOI: 10.1002/chem.201904044

  • PubMed Abstract: 
  • A DNA G-quadruplex adopting a (3+1) hybrid structure was modified in two adjacent syn positions of the antiparallel strand with anti-favoring 2'-deoxy-2'-fluoro-riboguanosine (FrG) analogs. The two substitutions promoted a structural rearrangement to ...

    A DNA G-quadruplex adopting a (3+1) hybrid structure was modified in two adjacent syn positions of the antiparallel strand with anti-favoring 2'-deoxy-2'-fluoro-riboguanosine (FrG) analogs. The two substitutions promoted a structural rearrangement to a topology with the 5'-terminal G residue located in the central tetrad and the two modified residues linked by a V-shaped zero-nucleotide loop. Strikingly, whereas a sugar pucker in the preferred north domain is found for both modified nucleotides, the FrG analog preceding the V-loop is forced to adopt the unfavored syn conformation in the new quadruplex fold. Apparently, a preferred C3'-endo sugar pucker within the V-loop architecture outweighs the propensity of the FrG analog to adopt an anti glycosidic conformation. Refolding into a V-loop topology is likewise observed for a sequence modified at corresponding positions with two riboguanosine substitutions. In contrast, 2'-F-arabinoguanosine analogs with their favored south-east sugar conformation do not support formation of the V-loop topology. Examination of known G-quadruplexes with a V-shaped loop highlights the critical role of the sugar conformation for this distinct structural motif.


    Organizational Affiliation

    Purdue University, Department of Medicinal Chemistry and Molecular Pharmacology, 47907, West Lafayette, UNITED STATES.,Universitat Greifswald, Institut für Biochemie, Felix-Hausdorff-Str. 4, 17487, Greifswald, GERMANY.,Ernst-Moritz-Arndt-Universität, Institut für Biochemie, Felix-Hausdorff-Str. 4, 17487, Greifswald, GERMANY.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
F1415A22synthetic construct
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
GF2
Query on GF2
A
DNA linkingC10 H13 F N5 O7 PDG
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 20 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2019-05-21 
  • Released Date: 2019-11-06 
  • Deposition Author(s): Haase, L., Weisz, K.

Funding OrganizationLocationGrant Number
German Research FoundationGermanyDFG WE 1933/15-1

Revision History 

  • Version 1.0: 2019-11-06
    Type: Initial release