Locating chemical modifications in RNA sequences through ribonucleases and LC-MS based analysis

Methods Enzymol. 2021:658:1-24. doi: 10.1016/bs.mie.2021.06.023. Epub 2021 Jul 27.

Abstract

Knowledge of the structural information is essential for understanding the functional details of modified RNA. Cellular non-coding RNA such as rRNA, tRNA and even viral RNAs contain a number of post-transcriptional modifications with varied degree of diversity and density. In this chapter, we discuss the use of a combination of biochemical and analytical tools such as ribonucleases and liquid chromatography coupled with mass spectrometry approaches for characterization of modified RNA. We present the protocols and alternate strategies for obtaining confident modified sequence information to facilitate the understanding of function.

Keywords: LC-MS; Oligonucleotide sequencing; Overlapping digestion products; Post-transcriptional modifications; RNA modification mapping; Ribonucleases.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Sequence
  • Chromatography, Liquid
  • RNA Processing, Post-Transcriptional
  • RNA* / genetics
  • RNA, Transfer / genetics
  • RNA, Transfer / metabolism
  • Ribonucleases* / metabolism
  • Tandem Mass Spectrometry

Substances

  • RNA
  • RNA, Transfer
  • Ribonucleases