Effects of Water on the Single-Chain Elasticity of Poly(U) RNA

Water, the dominant component under the physiological condition, is a complicated solvent which greatly affects the properties of solute molecules. Here, we utilize atomic force microscope-based single-molecule force spectroscopy to study the influence of water on the single-molecule elasticity of an unstructured single-stranded RNA (poly(U)). In nonpolar solvents, RNA presents its inherent elasticity, which is consistent with the theoretical single-chain elasticity calculated by quantum mechanics calculations. In aqueous buffers, however, an additional energy of 1.88 kJ/mol.base is needed for the stretching of the ssRNA chain. This energy is consumed by the bound water rearrangement (E-w) during chain elongation. Further experimental results indicate that the E-w value is uncorrelated to the salt concentrations and stretching velocity. The results obtained in an 8 M guanidine center dot HCl solution provide more evidence that the bound water molecules around RNA give rise to the observed deviation between aqueous and nonaqueous environments. Compared to synthetic water-soluble polymers, the value of E-w of RNA is much lower. The weak interference of water is supposed to be the precondition for the RNA secondary structure to exist in aqueous solution.