7XH9

Crystal structure of a dimeric interlocked parallel G-quadruplex

7XH9 の概要

• エントリーDOI: 10.2210/pdb7xh9/pdb
• 分子名称: DNA (5'-D(*GP*GP*GP*GP*TP*GP*GP*GP*CP*GP*GP*TP*GP*GP*GP*T)-3'), POTASSIUM ION, STRONTIUM ION, ... (4 entities in total)
• 機能のキーワード: g-quadruplex, interlocked, dna
• 由来する生物種: synthetic construct
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 10760.51

構造登録者

Ngo, K.H.,Liew, C.W.,Lattmann, S.,Winnerdy, F.R.,Phan, A.T. (登録日: 2022-04-07, 公開日: 2023-02-15, 最終更新日: 2023-11-29)

主引用文献

Ngo, K.H.,Liew, C.W.,Lattmann, S.,Winnerdy, F.R.,Phan, A.T.
Crystal structures of an HIV-1 integrase aptamer: Formation of a water-mediated A.G.G.G.G pentad in an interlocked G-quadruplex.
Biochem.Biophys.Res.Commun., 613:153-158, 2022

PubMed Abstract: 93del is a 16-nucleotide G-quadruplex-forming aptamer which can inhibit the activity of the HIV-1 integrase enzyme at nanomolar concentration. Previous structural analyses of 93del using NMR spectroscopy have shown that the aptamer forms an interlocked G-quadruplex structure in K solution. Due to its exceptional stability and unique topology, 93del has been used in many different studies involving DNA G-quadruplexes, such as DNA aptamer and multimer design, as well as DNA fluorescence research. To gain further insights on the structure of this unique aptamer, we have determined several high-resolution crystal structures of 93del and its variants. While confirming the overall dimeric interlocked G-quadruplex folding topology previously determined by NMR, our results reveal important detailed structural information, particularly the formation of a water-mediated A•G•G•G•G pentad. These insights allow us to better understand the formation of various structural elements in G-quadruplexes and should be useful for designing and manipulating G-quadruplex scaffolds with desired properties.

PubMed: 35561583
DOI: 10.1016/j.bbrc.2022.04.020

実験手法

X-RAY DIFFRACTION (1.63 Å)