6F4Z

2'F-araG modified quadruplex with flipped G-tract and central tetrad

• PDB DOI: https://doi.org/10.2210/pdb6F4Z/pdb
• BMRB: 34210
• NAKB: 6F4Z

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


• Deposited: 2017-11-30 Released: 2018-04-25 
• Deposition Author(s): Dickerhoff, J., Weisz, K.

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Experimental Data Snapshot

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

Literature

Fluorine-Mediated Editing of a G-Quadruplex Folding Pathway.

Dickerhoff, J., Weisz, K.

(2018) Chembiochem 19: 927-930

• PubMed: 29460996 
• DOI: https://doi.org/10.1002/cbic.201800099
• Primary Citation of Related Structures:  
  6F4Z


• PubMed Abstract: 
  

  A (3+1)-hybrid-type G-quadruplex was substituted within its central tetrad by a single 2'-fluoro-modified guanosine. Driven by the anti-favoring nucleoside analogue, a novel quadruplex fold with inversion of a single G-tract and conversion of a propeller loop into a lateral loop emerges. In addition, scalar couplings across hydrogen bonds demonstrate the formation of intra- and inter-residual F⋅⋅⋅H8-C8 pseudo-hydrogen bonds within the modified quadruplexes. Alternative folding can be rationalized by the impact of fluorine on intermediate species on the basis of a kinetic partitioning mechanism. Apparently, chemical or other environmental perturbations are able to redirect folding of a quadruplex, possibly modulating its regulatory role in physiological processes.

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Organizational Affiliation: 

Institut für Biochemie, Ernst-Moritz-Arndt-Universität Greifswald, Felix-Hausdorff-Strasse 4, 17487, Greifswald, Germany.

Biological Assembly 1  

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 6.99 kDa 
• Atom Count: 466 
• Modelled Residue Count: 22 
• Deposited Residue Count: 22 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*GP*GP*AP*TP*GP*GP*GP*AP*CP*AP*CP*AP*GP*(GFL)P*GP*GP*AP*CP*GP*GP*G)-3')	A	22	synthetic construct

Experimental Data & Validation

Experimental Data

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-04-25 
Deposition Author(s): Dickerhoff, J., Weisz, K.

Revision History  

• Version 1.0: 2018-04-25
  Type: Initial release
  
• Version 1.1: 2018-05-16
  Changes: Data collection, Database references
• Version 1.2: 2019-05-08
  Changes: Data collection
• Version 1.3: 2024-05-15
  Changes: Data collection, Database references