The DOI matches its Crossref record; 117 of the 117 references it cites were found in a registry or an index.
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 the citing paper
“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
In the citing paper
“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
Citations
Cites
The RNA moiety of ribonuclease P is the catalytic subunit of the enzyme
Guerrier-Takada, C., Gardiner, K., Marsh, T., Pace, N., & Altman, S. (1983) · Cell · doi:10.1016/0092-8674(83)90117-4 · Cited by 2,684
Cech, T. R., Zaug, A. J., & Grabowski, P. J. (1981) · Cell · doi:10.1016/0092-8674(81)90390-1 · Cited by 879
Pseudo-rotation in the hydrolysis of phosphate esters
Westheimer, F. H. (1968) · Accounts of Chemical Research · doi:10.1021/ar50003a002 · Cited by 772
Structural Features that Give Rise to the Unusual Stability of RNA Hairpins Containing GNRA Loops
Heus, H. A., & Pardi, A. (1991) · Science · doi:10.1126/science.1712983 · Cited by 618
Li, Y., & Breaker, R. R. (1999) · Journal of the American Chemical Society · doi:10.1021/ja990592p · Cited by 587
Highly Efficient Synthesis of Covalently Cross-Linked Peptide Helices by Ring-Closing Metathesis
Blackwell, H. E., & Grubbs, R. H. (1998) · Angewandte Chemie International Edition · doi:10.1002/(sici)1521-3773(19981217)37:23 · Cited by 575
Williams, N. H., Takasaki, B. K., Wall, M., & Chin, J. (1999) · Accounts of Chemical Research · doi:10.1021/ar9500877 · Cited by 550
Relationship between internucleotide linkage geometry and the stability of RNA
Soukup, G. A., & Breaker, R. R. (1999) · RNA · doi:10.1017/s1355838299990891 · Cited by 549
The Intervening Sequence RNA of Tetrahymena Is an Enzyme
Zaug, A. J., & Cech, T. R. (1986) · Science · doi:10.1126/science.3941911 · Cited by 507
Oivanen, M., Kuusela, S., & Lönnberg, H. (1998) · Chemical Reviews · doi:10.1021/cr960425x · Cited by 438
Self-citation
Cited by
mRNA-lipid nanoparticle COVID-19 vaccines: structure and stability
Schoenmaker, L., Witzigmann, D., Kulkarni, J. A., Verbeke, R., Kersten, G., Jiskoot, W., & Crommelin, D. J. A. (2021) · International Journal of Pharmaceutics · doi:10.1016/j.ijpharm.2021.120586 · Cited by 1,566
Addressing the Cold Reality of mRNA Vaccine Stability
Crommelin, D. J. A., Anchordoquy, T. J., Volkin, D. B., Jiskoot, W., & Mastrobattista, E. (2021) · Journal of Pharmaceutical Sciences · doi:10.1016/j.xphs.2020.12.006 · Cited by 517
Combinatorial optimization of mRNA structure, stability, and translation for RNA-based therapeutics
Leppek, K., Byeon, G. W., Kladwang, W., Wayment-Steele, H. K., Kerr, C. H., Xu, A. F., Kim, D. S., Topkar, V. V., Choe, C., Rothschild, D., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-28776-w · Cited by 399
Combinatorial optimization of mRNA structure, stability, and translation for RNA-based therapeutics
Leppek, K., Byeon, G. W., Kladwang, W., Wayment-Steele, H. K., Kerr, C. H., Xu, A. F., Kim, D. S., Topkar, V. V., Choe, C., Rothschild, D., et al. (2021) · doi:10.1101/2021.03.29.437587 · Cited by 399
Synthetic metallonucleases for RNA cleavage
Morrow, J. R., & Iranzo, O. (2004) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2004.02.006 · Cited by 223
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
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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.
