6TC8

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

• PDB DOI: https://doi.org/10.2210/pdb6TC8/pdb
• NAKB: 6TC8
• BMRB: 34444

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


• Deposited: 2019-11-05 Released: 2020-03-25 
• Deposition Author(s): Haase, L., Weisz, K.
• Funding Organization(s): German Research Foundation

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Experimental Data Snapshot

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

Literature

Switching the type of V-loop in sugar-modified G-quadruplexes through altered fluorine interactions.

Haase, L., Weisz, K.

(2020) Chem Commun (Camb) 56: 4539-4542

• PubMed: 32202271 
• DOI: https://doi.org/10.1039/d0cc01285h
• Primary Citation of Related Structures:  
  6TC8, 6TCG


• PubMed Abstract: 
  

  Mixed 2'-F-riboguanosine and 2'-F-arabinoguanosine disubstitutions of a hybrid-type G-quadruplex are found to induce a refolding into two alternative structures with different types of V-loops upon positional exchange of the two G analogs. While conformational preferences of the incorporated G surrogates fail to fully account for the observed rearrangements, additional hydrogen bonds with a fluorine acceptor are suggested to be critical determinants of the two distinct V-loop conformers imposing different tetrad polarities.

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Organizational Affiliation: 

Institut für Biochemie, Universität Greifswald, Felix-Hausdorff-Str. 4, D-17489 Greifswald, Germany. [e-mail].

Biological Assembly 1  

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

Macromolecule Content

• Total Structure Weight: 7.01 kDa 
• Atom Count: 467 
• 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*(GFL)P*(GF2)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 & Funding Information

Deposition Data

• Released Date: 2020-03-25 
Deposition Author(s): Haase, L., Weisz, K.

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Funding Organization	Location	Grant Number
German Research Foundation	Germany	DFG WE 1933/15-1

Revision History  

• Version 1.0: 2020-03-25
  Type: Initial release
  
• Version 1.1: 2020-04-01
  Changes: Database references
• Version 1.2: 2020-05-06
  Changes: Database references