7ZEK

Structure of a hybrid-type G-quadruplex with a snapback loop (hybrid 1R')

7ZEK の概要

• エントリーDOI: 10.2210/pdb7zek/pdb
• NMR情報: BMRB: 34721
• 分子名称: DNA (5'-D(*(DG5)P*GP*CP*TP*AP*(BG)P*GP*GP*TP*CP*AP*GP*GP*GP*TP*GP*GP*GP*TP*CP*AP*(DG3))-3') (1 entity in total)
• 機能のキーワード: hybrid g-quadruplex, snapback loop, dna
• 由来する生物種: synthetic construct
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 6928.37

構造登録者

Jana, J.,Vianney, Y.M.,Schroeder, N.,Weisz, K. (登録日: 2022-03-31, 公開日: 2022-06-22, 最終更新日: 2024-06-19)

主引用文献

Jana, J.,Vianney, Y.M.,Schroder, N.,Weisz, K.
Guiding the folding of G-quadruplexes through loop residue interactions.
Nucleic Acids Res., 50:7161-7175, 2022

PubMed Abstract: A G-rich sequence was designed to allow folding into either a stable parallel or hybrid-type topology. With the parent sequence featuring coexisting species, various related sequences with single and double mutations and with a shortened central propeller loop affected the topological equilibrium. Two simple modifications, likewise introduced separately to all sequences, were employed to lock folds into one of the topologies without noticeable structural alterations. The unique combination of sequence mutations, high-resolution NMR structural information, and the thermodynamic stability for both topological competitors identified critical loop residue interactions. In contrast to first loop residues, which are mostly disordered and exposed to solvent in both propeller and lateral loops bridging a narrow groove, the last loop residue in a lateral three-nucleotide loop is engaged in stabilizing stacking interactions. The propensity of single-nucleotide loops to favor all-parallel topologies by enforcing a propeller-like conformation of an additional longer loop is shown to result from their preference in linking two outer tetrads of the same tetrad polarity. Taken together, the present studies contribute to a better structural and thermodynamic understanding of delicate loop interactions in genomic and artificially designed quadruplexes, e.g. when employed as therapeutics or in other biotechnological applications.

PubMed: 35758626
DOI: 10.1093/nar/gkac549

実験手法

SOLUTION NMR