6SX6

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

Summary for 6SX6

• Entry DOI: 10.2210/pdb6sx6/pdb
• NMR Information: BMRB: 34436
• Descriptor: GCn (1 entity in total)
• Functional Keywords: g-quadruplex, a(gggg)a hexad, gcgc-quartet, 5'-gc ends, dna
• Biological source: synthetic construct
• Total number of polymer chains: 2
• Total formula weight: 7666.98

Authors

Pavc, D.,Wang, B.,Spindler, L.,Drevensek-Olenik, I.,Plavec, J.,Sket, P. (deposition date: 2019-09-25, release date: 2020-07-22, Last modification date: 2024-05-15)

Primary citation

Pavc, D.,Wang, B.,Spindler, L.,Drevensek-Olenik, I.,Plavec, J.,Sket, P.
GC ends control topology of DNA G-quadruplexes and their cation-dependent assembly.
Nucleic Acids Res., 48:2749-2761, 2020

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.

PubMed: 31996902
DOI: 10.1093/nar/gkaa058

Experimental method

SOLUTION NMR