Vibrio Vulnificus Adenine Riboswitch Aptamer Domain, Synthesized by Position-selective Labeling of RNA (PLOR), in Complex with Adenine

Experimental Data Snapshot

  • Resolution: 2.21 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.210 

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

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

(2015) Nature 522: 368-372

  • DOI: https://doi.org/10.1038/nature14352
  • Primary Citation of Related Structures:  

  • PubMed 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.

  • Organizational Affiliation

    JILA, National Institute of Standards and Technology and Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309, USA.

Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains LengthOrganismImage
Vibrio Vulnificus Adenine RiboswitchA [auth X]71Vibrio vulnificus
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.21 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.210 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.482α = 90
b = 154.682β = 90
c = 25.178γ = 90
Software Package:
Software NamePurpose
XDSdata scaling
Cootmodel building
PDB_EXTRACTdata extraction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-05-06
    Type: Initial release
  • Version 1.1: 2015-05-27
    Changes: Database references
  • Version 1.2: 2015-07-01
    Changes: Database references
  • Version 1.3: 2017-11-22
    Changes: Database references, Derived calculations, Refinement description, Source and taxonomy
  • Version 1.4: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description