ArticleFEBS open bio2014
Hammerhead ribozyme activity and oligonucleotide duplex stability in mixed solutions of water and organic compounds.
Article in FEBS open bio, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed, 31 citations in OpenAlex.
- Effects of Molecular Crowding on the Structure, Folding, Stability, and Catalysis of RNA.Sub-cellular biochemistry · 2025Review
- Apolar chemical environments compact unfolded RNAs and can promote folding.Biophysical reports · 2021Article
- Enzymatic Reactions inside Biological Condensates.Journal of molecular biology · 2021Review
- Bulky cations greatly increase the turnover of a native hammerhead ribozyme.RSC advances · 2019Article
- Optimal molecular crowding accelerates group II intron folding and maximizes catalysis.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- Compartmentalised RNA catalysis in membrane-free coacervate protocells.Nature communications · 2018Article
- Thermal stability and conformation of DNA and proteins under the confined condition in the matrix of hydrogels.Molecular biology reports · 2018Article
- Pursuing origins of (poly)ethylene glycol-induced G-quadruplex structural modulations.Nucleic acids research · 2018Article
- Article
- Entropic stabilization of folded RNA in crowded solutions measured by SAXS.Nucleic acids research · 2016Article
- Thermal Stability of RNA Structures with Bulky Cations in Mixed Aqueous Solutions.Biophysical journal · 2016Article
- The structural stability and catalytic activity of DNA and RNA oligonucleotides in the presence of organic solvents.Biophysical reviews · 2016Review
- Effects of background anionic compounds on the activity of the hammerhead ribozyme in Mg(2+)-unsaturated solutions.Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry · 2015Article
- Roles of the amino group of purine bases in the thermodynamic stability of DNA base pairing.Molecules (Basel, Switzerland) · 2014Article
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Nucleic acids are useful for biomedical targeting and sensing applications in which the molecular environment is different from that of a dilute aqueous solution. In this study, the influence of various types of mixed solutions of water and water-soluble organic compounds on RNA was investigated by measuring the catalytic activity of the hammerhead ribozyme and the thermodynamic stability of an oligonucleotide duplex. The compounds with a net neutral charge, such as poly(ethylene glycol), small primary alcohols, amide compounds, and aprotic solvent molecules, added at high concentrations changed the ribozyme-catalyzed RNA cleavage rate, with the magnitude of the effect dependent on the NaCl concentration. These compounds also changed the thermodynamic stability of RNA base pairs of an oligonucleotide duplex and its dependence on the NaCl concentration. Specific interactions with RNA molecules and reduced water activity could account for the inhibiting effects on the ribozyme catalysis and destabilizing effects on the duplex stability. The salt concentration dependence data correlated with the dielectric constant, but not with water activity, viscosity, and the size of organic compounds. This observation suggests the significance of the dielectric constant effects on the RNA reactions under molecular crowding conditions created by organic compounds.
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