Cited by 68RNA and protein synthesis mechanismsDNA and Nucleic Acid ChemistryChemical Reaction Mechanisms

The effect of secondary structure on cleavage of the phosphodiester bonds of RNA

Mikkola, Satu, Kaukinen, Ulla, Lönnberg, Harri·2001·Cell Biochemistry and Biophysics

Abstract

This review discusses the effects the secondary structure of an RNA molecule has on the inherent reactivity of its phosphodiester bonds, and on the catalytic activity of metal ion-based cleaving agents. The basic principles of the intramolecular transesterification of RNA phosphodiester bonds, particularly cleavage, are first briefly described. Studies of the structural effects on the cleavage, in the absence and in the presence of metal ion catalysts, are then reviewed, and the sources of the reactivity differences observed in different structures are discussed.

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Crossref · 10.1385/cbb:34:1:95

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117 of 117 references verified0 citation errors · 0 not checkable

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  • We obtained single-nucleotide-resolution measurements of 3030 RNA fragments using In-line-seq.

    “In particular, we obtained single-nucleotide-resolution measurements of 3030 RNA fragments using In-line-seq, a version of a low-bias ligation and reverse transcription protocol (MAP-seq)64 adapted here for in-line hydrolysis profiles65 (Fig. 3B).”
  • The base sequence and secondary structure of mRNA influence the rate of hydrolysis.

    “In two publications on mRNA hydrolysis the authors state that the base sequence and secondary structure of mRNA influence the rate of hydrolysis (Kaukinen et al., 2002, Mikkola et al., 2001).”

    From mRNA-lipid nanoparticle COVID-19 vaccines: structure and stability (2021) · cites this paper as Mikkola et al., 2001

  • Base-stacking may decrease the cleavage rate of phosphodiester bonds.

    “Specifically, base-stacking may decrease the cleavage rate of phosphodiester bonds.”

    From mRNA-lipid nanoparticle COVID-19 vaccines: structure and stability (2021) · cites this paper as Mikkola et al., 2001

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Authors
Mikkola, S., Kaukinen, U., & Lönnberg, H.
Affiliations
University of Turku (FI)
Venue
Cell Biochemistry and Biophysics
Published
2001
Volume
34
Issue
1
Pages
95-119
ISSN
1085-9195 (ISSN-L)
OpenAlex
W1980553137
Cited by
67
References
117
Citations by year
2026: 4 · 2025: 1 · 2024: 4 · 2023: 5 · 2022: 8 · 2021: 2 · 2020: 1 · 2019: 2 · 2018: 2 · 2017: 1 · 2016: 1 · 2015: 2 · 2014: 4
FWCI
1.04
Type
journal article
Language
en
Open access
closed
Locations
  • Cell Biochemistry and Biophysics (publishedVersion)
  • PubMed (publishedVersion)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA and Nucleic Acid Chemistry
  • Physical Sciences › Chemistry › Organic Chemistry › Chemical Reaction Mechanisms
Keywords
RNA secondary structure, phosphodiester bond cleavage, metal ion catalysis
MeSH terms
Base Sequence, Catalysis, Chemistry, Physical, Esterification, Hydrogen-Ion Concentration, Metals, Nucleic Acid Conformation, RNA, RNA, Double-Stranded, RNA, Transfer, RNA, Catalytic, Chemical Phenomena

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