RNA Design Principles for Riboswitches that Regulate RNase P-Mediated tRNA Processing

Methods Mol Biol. 2022;2518:179-202. doi: 10.1007/978-1-0716-2421-0_11.

Abstract

Riboswitches are an attractive target for the directed design of RNA-based regulators by in silico prediction. These noncoding RNA elements consist of an aptamer platform for the highly selective ligand recognition and an expression platform which controls gene activity typically at the level of transcription or translation. In previous work, we could successfully apply RNA folding prediction to implement a new riboswitch mechanism regulating processing of a tRNA by RNase P. In this contribution, we present detailed information about our pipeline consisting of in silico design combined with the biochemical analysis for the verification of the implemented mechanism. Furthermore, we discuss the applicability of the presented biochemical in vivo and in vitro methods for the characterization of other artificial riboswitches.

Keywords: Design score calculation; Ligand-dependent tRNA processing; RNA design; RNase P riboswitch; Riboswitch characterization.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Nucleic Acid Conformation
  • RNA / chemistry
  • RNA Folding
  • RNA, Transfer / chemistry
  • RNA, Transfer / genetics
  • Ribonuclease P / genetics
  • Riboswitch* / genetics

Substances

  • Riboswitch
  • RNA
  • RNA, Transfer
  • Ribonuclease P