Hammerhead ribozyme activity and oligonucleotide duplex stability in mixed solutions of water and organic compounds
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...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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Wiley
2014-01-01
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| Series: | FEBS Open Bio |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2211546314000643 |
| _version_ | 1818324680557199360 |
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| author | Shu-ichi Nakano Yuichi Kitagawa Daisuke Miyoshi Naoki Sugimoto |
| author_facet | Shu-ichi Nakano Yuichi Kitagawa Daisuke Miyoshi Naoki Sugimoto |
| author_sort | Shu-ichi Nakano |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-13T11:32:26Z |
| format | Article |
| id | doaj.art-3d7374bbf1c64b2bbaff4ee9ec364108 |
| institution | Directory Open Access Journal |
| issn | 2211-5463 |
| language | English |
| last_indexed | 2024-12-13T11:32:26Z |
| publishDate | 2014-01-01 |
| publisher | Wiley |
| record_format | Article |
| series | FEBS Open Bio |
| spelling | doaj.art-3d7374bbf1c64b2bbaff4ee9ec3641082022-12-21T23:47:53ZengWileyFEBS Open Bio2211-54632014-01-014C64365010.1016/j.fob.2014.06.009Hammerhead ribozyme activity and oligonucleotide duplex stability in mixed solutions of water and organic compoundsShu-ichi Nakano0Yuichi Kitagawa1Daisuke Miyoshi2Naoki Sugimoto3Department of Nanobiochemistry, Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, Kobe, JapanDepartment of Nanobiochemistry, Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, Kobe, JapanDepartment of Nanobiochemistry, Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, Kobe, JapanDepartment of Nanobiochemistry, Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, Kobe, JapanNucleic 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.http://www.sciencedirect.com/science/article/pii/S2211546314000643RNAEnzymeThermal stabilityMolecular crowdingDielectric constant |
| spellingShingle | Shu-ichi Nakano Yuichi Kitagawa Daisuke Miyoshi Naoki Sugimoto Hammerhead ribozyme activity and oligonucleotide duplex stability in mixed solutions of water and organic compounds FEBS Open Bio RNA Enzyme Thermal stability Molecular crowding Dielectric constant |
| title | Hammerhead ribozyme activity and oligonucleotide duplex stability in mixed solutions of water and organic compounds |
| title_full | Hammerhead ribozyme activity and oligonucleotide duplex stability in mixed solutions of water and organic compounds |
| title_fullStr | Hammerhead ribozyme activity and oligonucleotide duplex stability in mixed solutions of water and organic compounds |
| title_full_unstemmed | Hammerhead ribozyme activity and oligonucleotide duplex stability in mixed solutions of water and organic compounds |
| title_short | Hammerhead ribozyme activity and oligonucleotide duplex stability in mixed solutions of water and organic compounds |
| title_sort | hammerhead ribozyme activity and oligonucleotide duplex stability in mixed solutions of water and organic compounds |
| topic | RNA Enzyme Thermal stability Molecular crowding Dielectric constant |
| url | http://www.sciencedirect.com/science/article/pii/S2211546314000643 |
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