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The Effect of Secondary Structure on Cleavage of the Phosphodiester Bonds of RNA
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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“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).”
From Combinatorial optimization of mRNA structure, stability, and translation for RNA-based therapeutics (2022) · cites this paper as [64]
In the citing paper
“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
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“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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Metadata
- 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 › Physical Organic Chemistry and Reaction Kinetics
- 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
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.