6GZK

Solution NMR structure of the tetramethylrhodamine (TMR) aptamer 3 in complex with 5-TAMRA

6GZK の概要

• エントリーDOI: 10.2210/pdb6gzk/pdb
• NMR情報: BMRB: 26842
• 分子名称: TMR3 (48-MER), 5-carboxy methylrhodamine (2 entities in total)
• 機能のキーワード: rna aptamer, rna-ligand complex, three-way junction, rna
• 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: 15925.69

構造登録者

Duchardt-Ferner, E.,Ohlenschlager, O.,Kreutz, C.R.,Wohnert, J. (登録日: 2018-07-04, 公開日: 2019-07-17, 最終更新日: 2024-05-15)

主引用文献

Duchardt-Ferner, E.,Juen, M.,Bourgeois, B.,Madl, T.,Kreutz, C.,Ohlenschlager, O.,Wohnert, J.
Structure of an RNA aptamer in complex with the fluorophore tetramethylrhodamine.
Nucleic Acids Res., 48:949-961, 2020

PubMed Abstract: RNA aptamers-artificially created RNAs with high affinity and selectivity for their target ligand generated from random sequence pools-are versatile tools in the fields of biotechnology and medicine. On a more fundamental level, they also further our general understanding of RNA-ligand interactions e. g. in regard to the relationship between structural complexity and ligand affinity and specificity, RNA structure and RNA folding. Detailed structural knowledge on a wide range of aptamer-ligand complexes is required to further our understanding of RNA-ligand interactions. Here, we present the atomic resolution structure of an RNA-aptamer binding to the fluorescent xanthene dye tetramethylrhodamine. The high resolution structure, solved by NMR-spectroscopy in solution, reveals binding features both common and different from the binding mode of other aptamers with affinity for ligands carrying planar aromatic ring systems such as the malachite green aptamer which binds to the tetramethylrhodamine related dye malachite green or the flavin mononucleotide aptamer.

PubMed: 31754719
DOI: 10.1093/nar/gkz1113

実験手法

SOLUTION NMR