The structural stability and catalytic activity of DNA and RNA oligonucleotides in the presence of organic solvents

Abstract

Organic solvents and apolar media are used in the studies of nucleic acids to modify the conformation and function of nucleic acids, to improve solubility of hydrophobic ligands, to construct molecular scaffolds for organic synthesis, and to study molecular crowding effects. Understanding how organic solvents affect nucleic acid interactions and identifying the factors that dominate solvent effects are important for the creation of oligonucleotide-based technologies. This review describes the structural and catalytic properties of DNA and RNA oligonucleotides in organic solutions and in aqueous solutions with organic cosolvents. There are several possible mechanisms underlying the effects of organic solvents on nucleic acid interactions. The reported results emphasize the significance of the osmotic pressure effect and the dielectric constant effect in addition to specific interactions with nucleic acid strands. This review will serve as a guide for the selection of solvent systems based on the purpose of the nucleic acid-based experiments.

Keywords: DNAzyme; Dielectric constant; Molecular crowding; Oligonucleotide; Organic solvent; Ribozyme.

Fig. 1

a Relative dielectric constants ε _r of organic solutions and those of cells, DNAs, and proteins (Asami et al. ; Lamm and Pack ; Young et al. ; Pitera et al. ; Cuervo et al. 2014). b Solvent properties of water, organic solvents, and mixed aqueous solutions with organic cosolvents

Fig. 2

a Organic solvents used for the preparation of mixed aqueous solutions. The properties of water activity a _w and relative dielectric constant ε _r of 20 wt% solutions are indicated. b Values of the water activity and the relative dielectric constant determined for the 20 wt% solutions of organic cosolvents containing 1 M NaCl (Nakano et al. 2004, 2012a)

Fig. 3

The NaCl concentration dependence of the stability of DNA and RNA structures relative to the dependence in the absence of cosolvents (S _K ^c/S _K ^w) against the dielectric constant (ε _r or ε _r ⁻¹) of mixed solutions with organic cosolvents at 5–50 wt%. The data are derived from the reports for a 20-mer DNA that forms a hairpin (blue) (Karimata et al. 2007), 18-mer DNA duplex and hairpin (purple) (Nakano et al. 2008), 13-mer DNA duplexes (green) (Nakano and Sugimoto 2014), an 11-mer RNA duplex (black) (Nakano et al. 2014b), and a 9-mer RNA duplex (red; our unpublished results). The data obtained in water solution are indicated by open circles

Fig. 4

a Effect of the charge spacing distance b on the degree of interaction with monovalent cations Ψ in the medium of ε _r = 80 (black) or 60 (red) at 25 °C. b Effect of ε _r on Ψ for the charge spacing distance 0.17 nm (black), 0.43 nm (blue), or 0.39 nm (red). c The reaction cycle for the formation of a duplex (ds) from a single strand (ss) in water solution (superscript w) or mixed solution with a low dielectric constant cosolvent (superscript c). d Effect of the ε _r on the change in Ψ during the duplex formation (b _ds = 0.17 nm) from a single strand of b _ss = 0.43 nm (blue) or 0.39 nm (red). e Effect of the b _ss on the ∆Ψ in the medium of ε _r = 60 relative to that in ε _r = 80 with an assumption that the value of b _ds = 0.17 nm is invariant. The data points for b _ss = 0.43 and 0.39 nm described in the text are marked by closed circles. f The curve fits to the data in Fig. 3 using a linear approximation of b _ss as a function of ε _r. The broken lines represent the theoretical curve generated using a constant value 0.39 nm for b _ss

Fig. 5

a The ribozyme structures described in the text and their cleavage sites (red arrows). b Plots of the NaCl concentration dependence of the cleavage rate constant of a hammerhead ribozyme relative to the dependence in the absence of cosolvents (S _k ^c/S _k ^w) against the dielectric constant (ε _r or ε _r ⁻¹) of mixed solutions in the amount of 10 or 20 wt% cosolvents (Nakano et al. 2014b). The curve fits are drawn based on the calculation performed in Fig. 4f. c The reaction cycle for the formation of the catalytically active form of ribozymes in water solution and a mixed solution with a low dielectric constant cosolvent