2N9Q | pdb_00002n9q

Photoswitchable G-quadruplex

• PDB DOI: https://doi.org/10.2210/pdb2N9Q/pdb
• BMRB: 25915
• NAKB: 2N9Q

• Classification: DNA
• Mutation(s): No 


• Deposited: 2015-12-02 Released: 2016-02-17 
• Deposition Author(s): Thevarpadam, J., Bessi, I., Binas, O., Goncalves, D.P.N., Slavov, C., Jonker, H.R.A., Richter, C., Wachtveitl, J., Schwalbe, H., Heckel, A.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Literature

Photoresponsive Formation of an Intermolecular Minimal G-Quadruplex Motif.

Thevarpadam, J., Bessi, I., Binas, O., Goncalves, D.P., Slavov, C., Jonker, H.R., Richter, C., Wachtveitl, J., Schwalbe, H., Heckel, A.

(2016) Angew Chem Int Ed Engl 55: 2738-2742

• PubMed: 26805928 
• DOI: https://doi.org/10.1002/anie.201510269
• Primary Citation Related Structures: 
  2N9Q


• PubMed Abstract: 
  

  The ability of three different bifunctional azobenzene linkers to enable the photoreversible formation of a defined intermolecular two-tetrad G-quadruplex upon UV/Vis irradiation was investigated. Circular dichroism and NMR spectroscopic data showed the formation of G-quadruplexes with K(+)  ions at room temperature in all three cases with the corresponding azobenzene linker in an E conformation. However, only the para-para-substituted azobenzene derivative enables photoswitching between a nonpolymorphic, stacked, tetramolecular G-quadruplex and an unstructured state after E-Z isomerization.

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Organizational Affiliation: 
• Goethe University Frankfurt, Institute for Organic Chemistry and Chemical Biology, Buchmann Institute for Molecular Life Sciences, Max-von-Laue-Strasse 9, 60438, Frankfurt, Germany.
Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Max-von-Laue-Strasse 9, 60438, Frankfurt, Germany.
Institute for Physical and Theoretical Chemistry, Max-von-Laue-Strasse 7, 60438, Frankfurt, Germany.
Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Max-von-Laue-Strasse 9, 60438, Frankfurt, Germany. [e-mail].
Goethe University Frankfurt, Institute for Organic Chemistry and Chemical Biology, Buchmann Institute for Molecular Life Sciences, Max-von-Laue-Strasse 9, 60438, Frankfurt, Germany. [e-mail].

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 6.42 kDa 
• Atom Count: 427 
• Modeled Residue Count: 20 
• Deposited Residue Count: 20 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*GP*(AZW)P*GP*G)-3')	A, B, C, D	5	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
K	E [auth A], F [auth A], G [auth C]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-02-17 
Deposition Author(s): Thevarpadam, J., Bessi, I., Binas, O., Goncalves, D.P.N., Slavov, C., Jonker, H.R.A., Richter, C., Wachtveitl, J., Schwalbe, H., Heckel, A.

Revision History  

• Version 1.0: 2016-02-17
  Type: Initial release
  
• Version 1.1: 2016-03-02
  Changes: Database references
• Version 1.2: 2023-06-14
  Changes: Data collection, Database references, Derived calculations, Other
• Version 1.3: 2024-05-15
  Changes: Data collection, Database references