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

A hybrid solid–liquid phase transcription method and automated robotic platform synthesizes position-specific, fluorescence- or isotope-labelled RNA. Selective labeling of RNA molecules The lack of a scaleable method of incorporating modified or labelled nucleotides into specific positions in RNA molecules has hampered RNA structural and dynamics studies. Yun-Xing Wang and colleagues now report an automated hybrid solid–liquid phase transcription process for the synthesis of position-specific, fluorescence- or isotope-labelled RNA. Labelling of a riboswitch demonstrates no effect on folding but does reveal a number of conformational states. As well as facilitating biochemical and biophysical studies, this labelling protocol, termed position-selective labelling of RNA (PLOR), may be used to develop biosensors and diagnostics. 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 1 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 dy