6SYK | pdb_00006syk

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 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.
University of Ljubljana, Faculty of Chemistry and Chemical Technology, 1000 Ljubljana, Slovenia.
University of Maribor, Faculty of Mechanical Engineering, 2000 Maribor, Slovenia.
Department of Complex Matter, Jozef Stefan Institute, 1000 Ljubljana, Slovenia.
University of Ljubljana, Faculty of Mathematics and Physics, 1000 Ljubljana, Slovenia.
EN-FIST Center of Excellence, 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 
• Modeled 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