6M05

Trimolecular G-quadruplex

Summary for 6M05

• Entry DOI: 10.2210/pdb6m05/pdb
• Descriptor: DNA (5'-D(*GP*TP*TP*AP*GP*G)-3') (1 entity in total)
• Functional Keywords: trimolecular g-quadruplex, human, tolerance, dna
• Biological source: Homo sapiens
• Total number of polymer chains: 3
• Total formula weight: 5592.76

Authors

Jing, H.T.,Fu, W.Q.,Zhang, N. (deposition date: 2020-02-20, release date: 2021-01-20, Last modification date: 2024-05-15)

Primary citation

Jing, H.,Fu, W.,Hu, W.,Xu, S.,Xu, X.,He, M.,Liu, Y.,Zhang, N.
NMR structural study on the self-trimerization of d(GTTAGG) into a dynamic trimolecular G-quadruplex assembly preferentially in Na+ solution with a moderate K+ tolerance.
Nucleic Acids Res., 49:2306-2316, 2021

PubMed Abstract: Vast G-quadruplexes (GQs) are primarily folded by one, two, or four G-rich oligomers, rarely with an exception. Here, we present the first NMR solution structure of a trimolecular GQ (tri-GQ) that is solely assembled by the self-trimerization of d(GTTAGG), preferentially in Na+ solution tolerant to an equal amount of K+ cation. Eight guanines from three asymmetrically folded strands of d(GTTAGG) are organized into a two-tetrad core, which features a broken G-column and two width-irregular grooves. Fast strand exchanges on a timescale of second at 17°C spontaneously occur between folded tri-GQ and unfolded single-strand of d(GTTAGG) that both species coexist in dynamic equilibrium. Thus, this tri-GQ is not just simply a static assembly but rather a dynamic assembly. Moreover, another minor tetra-GQ that has putatively tetrameric (2+2) antiparallel topology becomes noticeable only at an extremely high strand concentration above 18 mM. The major tri-GQ and minor tetra-GQ are considered to be mutually related, and their reversible interconversion pathways are proposed accordingly. The sequence d(GTTAGG) could be regarded as either a reading frame shifted single repeat of human telomeric DNA or a 1.5 repeat of Bombyx mori telomeric DNA. Overall, our findings provide new insight into GQs and expect more functional applications.

PubMed: 33524157
DOI: 10.1093/nar/gkab028

Experimental method

SOLUTION NMR