High-density functional-RNA arrays as a versatile platform for studying RNA-based interactions

Jack Phillips, Louise Butt, Charlotte Henderson, Martin Adrian Devonshire, Jess Healy, Stuart J. Conway, Nicolas Locker, Andrew Pickford, Helen Vincent, Anastasia Callaghan

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Abstract

We are just beginning to unravel the myriad of interactions in which non-coding RNAs participate. The intricate RNA interactome is the foundation of many biological processes, including bacterial virulence and human disease, and represents unexploited resources for the development of potential therapeutic interventions. However, identifying specific associations of a given RNA from the multitude of possible binding partners within the cell requires robust high-throughput systems for their rapid screening. Here, we present the first demonstration of functional-RNA arrays as a novel platform technology designed for the study of such interactions using immobilised, active RNAs. We have generated high-density RNA arrays by an innovative method involving surface-capture of in vitro transcribed RNAs. This approach has significant advantages over existing technologies, particularly in its versatility in regards to binding partner character. Indeed, proof-of-principle application of RNA arrays to both RNA-small molecule and RNA-RNA pairings is demonstrated, highlighting their potential as a platform technology for mapping RNA-based networks and for pharmaceutical screening. Furthermore, the simplicity of the method supports greater
user-accessibility over currently available technologies. We anticipate that functional-RNA arrays will find broad utility in the expanding field of RNA characterisation.
Original languageEnglish
Article numbere86
Number of pages10
JournalNucleic Acids Research
Volume46
Issue number14
Early online date28 May 2018
DOIs
Publication statusPublished - 21 Aug 2018

Keywords

  • RCUK
  • BBSRC
  • BB/I532988/1

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