PDBsum entry 4xnr

RNA

PDB id: 4xnr

Contents

DNA/RNA

Ligands

ADE

Metals

_MG ×6

Waters ×64

PDB id:

4xnr

Name:

RNA

Title:

Vibrio vulnificus adenine riboswitch aptamer domain, synthesized by position-selective labeling of RNA (plor), in complex with adenine

Structure:

Vibrio vulnificus adenine riboswitch. Chain: x. Engineered: yes

Source:

Synthetic: yes. Vibrio vulnificus. Organism_taxid: 672

Resolution:

2.21Å R-factor: 0.210 R-free: 0.220

Authors:

J.Zhang,Y.Liu,Y.-X.Wang,A.R.Ferre-D'Amare

Key ref:

Y.Liu et al. (2015). Synthesis and applications of RNAs with position-selective labelling and mosaic composition. Nature, 522, 368-372. PubMed id: 25938715 DOI: 10.1038/nature14352

Date:

16-Jan-15 Release date: 06-May-15

DNA/RNA chain

G-G-G-A-A-G-A-U-A-U-A-A-U-C-C-U-A-A-U-G-A-U-A-U-G-G-U-U-U-G-G-G-A-G-U-U-U-C-U- 71 bases

DOI no: 10.1038/nature14352

Nature 522:368-372 (2015)

PubMed id: 25938715

Synthesis and applications of RNAs with position-selective labelling and mosaic composition.

Y.Liu, E.Holmstrom, J.Zhang, P.Yu, J.Wang, M.A.Dyba, D.Chen, J.Ying, S.Lockett, D.J.Nesbitt, A.R.Ferré-D'Amaré, R.Sousa, J.R.Stagno, Y.X.Wang.

ABSTRACT

Knowledge of the structure and dynamics of RNA molecules is critical to understanding their many biological functions. Furthermore, synthetic RNAs have applications as therapeutics and molecular sensors. Both research and technological applications of RNA would be dramatically enhanced by methods that enable incorporation of modified or labelled nucleotides into specifically designated positions or regions of RNA. However, the synthesis of tens of milligrams of such RNAs using existing methods has been impossible. Here we develop a hybrid solid-liquid phase transcription method and automated robotic platform for the synthesis of RNAs with position-selective labelling. We demonstrate its use by successfully preparing various isotope- or fluorescently labelled versions of the 71-nucleotide aptamer domain of an adenine riboswitch for nuclear magnetic resonance spectroscopy or single-molecule Förster resonance energy transfer, respectively. Those RNAs include molecules that were selectively isotope-labelled in specific loops, linkers, a helix, several discrete positions, or a single internal position, as well as RNA molecules that were fluorescently labelled in and near kissing loops. These selectively labelled RNAs have the same fold as those transcribed using conventional methods, but they greatly simplify the interpretation of NMR spectra. The single-position isotope- and fluorescently labelled RNA samples reveal multiple conformational states of the adenine riboswitch. Lastly, we describe a robotic platform and the operation that automates this technology. Our selective labelling method may be useful for studying RNA structure and dynamics and for making RNA sensors for a variety of applications including cell-biological studies, substance detection, and disease diagnostics.