6SYK

Guanine-rich oligonucleotide with 5'- and 3'-GC ends form G-quadruplex with A(GGGG)A hexad, GCGC- and G-quartets and two symmetric GG and AA base pair

• PDB DOI: https://doi.org/10.2210/pdb6SYK/pdb
• NAKB: 6SYK
• BMRB: 34438

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


• Deposited: 2019-09-30 Released: 2020-07-29 
• Deposition Author(s): Pavc, D., Wang, B., Spindler, L., Drevensek-Olenik, I., Plavec, J., Sket, P.
• Funding Organization(s): Slovenian Research Agency

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 10 
• Selection Criteria: structures with the least restraint violations 

Literature

GC ends control topology of DNA G-quadruplexes and their cation-dependent assembly.

Pavc, D., Wang, B., Spindler, L., Drevensek-Olenik, I., Plavec, J., Sket, P.

(2020) Nucleic Acids Res 48: 2749-2761

• PubMed: 31996902 
• DOI: https://doi.org/10.1093/nar/gkaa058
• Primary Citation of Related Structures:  
  6SX6, 6SYK


• PubMed Abstract: 
  

  GCn and GCnCG, where n = (G2AG4AG2), fold into well-defined, dimeric G-quadruplexes with unprecedented folding topologies in the presence of Na+ ions as revealed by nuclear magnetic resonance spectroscopy. Both G-quadruplexes exhibit unique combination of structural elements among which are two G-quartets, A(GGGG)A hexad and GCGC-quartet. Detailed structural characterization uncovered the crucial role of 5'-GC ends in formation of GCn and GCnCG G-quadruplexes. Folding in the presence of 15NH4+ and K+ ions leads to 3'-3' stacking of terminal G-quartets of GCn G-quadruplexes, while 3'-GC overhangs in GCnCG prevent dimerization. Results of the present study expand repertoire of possible G-quadruplex structures. This knowledge will be useful in DNA sequence design for nanotechnological applications that may require specific folding topology and multimerization properties.

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Organizational Affiliation: 

Slovenian NMR Center, National Institute of Chemistry, 1000 Ljubljana, Slovenia.

Biological Assembly 1  

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

Biological Assembly Evidence: native gel electrophoresis

Macromolecule Content

• Total Structure Weight: 8.9 kDa 
• Atom Count: 594 
• Modelled Residue Count: 28 
• Deposited Residue Count: 28 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
GCnCG	A, B	14	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 10 
• Selection Criteria: structures with the least restraint violations 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-07-29 
Deposition Author(s): Pavc, D., Wang, B., Spindler, L., Drevensek-Olenik, I., Plavec, J., Sket, P.

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Funding Organization	Location	Grant Number
Slovenian Research Agency	Slovenia	--

Revision History  

• Version 1.0: 2020-07-29
  Type: Initial release
  
• Version 1.1: 2024-05-15
  Changes: Data collection, Database references