Conformation and the sodium ion condensation on DNA and RNA structures in the presence of a neutral cosolute as a mimic of the intracellular media

Abstract

Water-soluble neutral cosolutes can be used to quantify biomolecular properties in the particular molecular environment occurring in a cell. We studied the conformation and the thermal stability of DNA and RNA structures in the presence of PEG [poly(ethylene glycol)] and smaller cosolutes of glycerol, ethylene glycol, 1,3-propanediol, 2-methoxyethanol, and 1,2-dimethoxyethane. Although the neutral cosolutes destabilized the oligonucleotide duplex and the hairpin structures, the left-handed Z-form duplex was more energetically favored in the cosolute-containing solutions. These observations were due to the contribution of water molecule on the nucleotide structure formations because the cosolutes act as an osmolyte to reduce the water activity of a solution. Moreover, the sodium ion condensation for the duplex and the hairpin formations was reduced in the presence of PEG, while that for the transition from the B-form to the Z-form was unaltered. The CD (circular dichroism) and EPR (electron paramagnetic resonance) spectra demonstrated that the cosolutes changed the helical conformation of the unstructured oligonucleotides, but not those of the ordered structures. The results of the favorable formation of the noncanonical nucleotide structures, and minimized conformational and thermal perturbations of the ordered nucleotide structures in the cosolute-containing solutions implicate the significance of the intracellular environment on DNA and RNA structures in a cell.