7QUA

Duplex RNA containing Xanthosine-Cytosine base pairs

7QUA の概要

• エントリーDOI: 10.2210/pdb7qua/pdb
• 関連するPDBエントリー: 7QSH 7QTN
• 分子名称: RNA (5'-R(*CP*GP*CP*GP*(XAN)P*AP*UP*UP*AP*GP*CP*G)-3'), SODIUM ION, MAGNESIUM ION, ... (4 entities in total)
• 機能のキーワード: rna, modified base
• 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: 3963.94

構造登録者

Ennifar, E.,Micura, R. (登録日: 2022-01-17, 公開日: 2023-01-25, 最終更新日: 2024-02-07)

主引用文献

Mair, S.,Erharter, K.,Renard, E.,Brillet, K.,Brunner, M.,Lusser, A.,Kreutz, C.,Ennifar, E.,Micura, R.
Towards a comprehensive understanding of RNA deamination: synthesis and properties of xanthosine-modified RNA.
Nucleic Acids Res., 50:6038-6051, 2022

PubMed Abstract: Nucleobase deamination, such as A-to-I editing, represents an important posttranscriptional modification of RNA. When deamination affects guanosines, a xanthosine (X) containing RNA is generated. However, the biological significance and chemical consequences on RNA are poorly understood. We present a comprehensive study on the preparation and biophysical properties of X-modified RNA. Thermodynamic analyses revealed that base pairing strength is reduced to a level similar to that observed for a G•U replacement. Applying NMR spectroscopy and X-ray crystallography, we demonstrate that X can form distinct wobble geometries with uridine depending on the sequence context. In contrast, X pairing with cytidine occurs either through wobble geometry involving protonated C or in Watson-Crick-like arrangement. This indicates that the different pairing modes are of comparable stability separated by low energetic barriers for switching. Furthermore, we demonstrate that the flexible pairing properties directly affect the recognition of X-modified RNA by reverse transcription enzymes. Primer extension assays and PCR-based sequencing analysis reveal that X is preferentially read as G or A and that the ratio depends on the type of reverse transcriptase. Taken together, our results elucidate important properties of X-modified RNA paving the way for future studies on its biological significance.

PubMed: 35687141
DOI: 10.1093/nar/gkac477

実験手法

X-RAY DIFFRACTION (1 Å)