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

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.
Priti Thakur 1,  Scott Abernathy 1,  Patrick A Limbach 1,  Balasubrahmanyam Addepalli 2
Affiliations

Affiliations

  • 1 Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, OH, United States.
  • 2 Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, OH, United States. Electronic address: [email protected].
PMID: 34517943 DOI: 10.1016/bs.mie.2021.06.023
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.

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