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

Nucleic Acids Research
Jack O PhillipsAnastasia J Callaghan

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 immobilized, 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 use...Continue Reading

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Citations

Sep 29, 2019·Scientific Reports·Stefan D KrämerGünter Roth
Jul 21, 2021·ACS Synthetic Biology·Charlotte A HendersonAnastasia J Callaghan
Aug 5, 2021·The Journal of International Medical Research·Shu-Hsien LinKing-Wah Chiu

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Methods Mentioned

BETA
RNA
in vitro transcription
RNA array
PCR
in
electrophoresis
affinity purification
antisense oligonucleotides
biosensor

Software Mentioned

Mfold
RNAfold

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