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 (<i><i>E</i></i>_w) during chain elongation. Further experimental results indicate that the <i>E</i>_w value is uncorrelated to the salt concentrations and stretching velocity. The results obtained in an 8 M guanidine·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 <i>E</i>_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

How Big Is Big Enough? Effect of Length and Shape of Side Chains on the Single-Chain Enthalpic Elasticity of a Macromolecule

Polymers with a carbon–carbon (C–C) backbone are an important class of polymers, which can be regarded as the derivatives of polyethylene (PE). To investigate the effect of side chains on the single-chain enthalpic elasticity (SCEE) of polymers with a C–C backbone, several polymers with pendants or side chains of different lengths and shapes have been studied by single-molecule AFM. We find that both length and shape of the side chains count: only the side chains that are both long and bulky (i.e., bulky dendrons of second or higher generation as side chains) affect the SCEE. Thus, only rare polymers have special SCEE. For the vast majority of polymers, the SCEE is identical to that of PE, which means that the SCEE is determined by the nature of the C–C backbone. It is expected that this conclusion can also be popularized to all polymers with various backbones. This study is an important update to the understanding of polymers at the single-chain level