Hammerhead ribozyme activity and oligonucleotide duplex stability in mixed solutions of water and organic compounds

Graphical abstract

Highlights

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  Molecular crowding effects on RNA were studied using various mixed solutions.

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  The effect of salt concentration on ribozyme catalytic rate was altered.

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  The effect of salt concentration on RNA duplex stability was altered.

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  Dielectric constant effects are important for RNA reactions.

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  A method to predict nucleic acid folding in non-dilute aqueous solutions is proposed.

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.