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Studying the Key Intermediate of RNA Autohydrolysis by Cryogenic Gas-Phase Infrared Spectroscopy

Kim Greis1,2, Carla Kirschbaum1,2, Martín I Taccone2

  • 1Institut für Chemie und Biochemie, Freie Universität Berlin, Arnimallee 22, 14195, Berlin, Germany.

Angewandte Chemie (International Ed. in English)
|March 1, 2022
PubMed

Insights

Researchers investigated messenger RNA (mRNA) fragmentation in the gas phase, mimicking solution-phase RNA degradation. They identified a five-membered cyclic phosphate intermediate, clarifying a key fragmentation pathway for modified RNA molecules.

Area of Science:

  • Biochemistry
  • Physical Chemistry
  • Spectroscopy

Background:

  • Messenger RNA (mRNA) vaccines are crucial, necessitating a deep understanding of modified RNA molecule behavior.
  • Advanced mass spectrometry is vital for analyzing RNA, but gas-phase fragmentation mechanisms remain unclear.
  • RNA degradation in solution via autohydrolysis is known, but analogous gas-phase processes require elucidation.

Purpose of the Study:

  • To investigate the gas-phase fragmentation mechanisms of RNA dinucleotides.
  • To identify intermediates and pathways involved in RNA backbone cleavage in the gas phase.
  • To explore the gas-phase induction of other condensed-phase RNA reactions, such as cytosine tautomerization.

Main Methods:

  • Generation of isolated RNA dinucleotides in the gas phase.
  • Investigation using cryogenic infrared spectroscopy within helium nanodroplets.
  • Complementary analysis using density functional theory (DFT) calculations.

Main Results:

  • Evidence for the formation of a five-membered cyclic phosphate intermediate during RNA backbone cleavage.
  • Exclusion of linear or six-membered cyclic structures as intermediates.
  • Successful induction of cytosine tautomerization in the gas phase, mirroring condensed-phase reactions.

Conclusions:

  • The five-membered cyclic phosphate intermediate is a key species in gas-phase RNA backbone cleavage.
  • Gas-phase fragmentation of RNA shares similarities with solution-phase autohydrolysis.
  • Cytosine tautomerization can be induced in the gas phase, highlighting universal molecular properties.
Keywords:
AutohydrolysisFragmentationInfrared SpectroscopyMass SpectrometryRNA

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