Hydration of nucleic acids

Summary

Introduction

It is common knowledge that living tissue contains around 70% water, that water is certainly a unique liquid, and consequently that water plays a crucial role in both the structures and functions of biological macromolecules. The native conformations of biomolecules result from a balance between various intra- and intermolecular forces, e.g., interatomic repulsions, dispersion forces, hydrogen bonding forces, electrostatic forces, torsional forces about covalent bonds, and forces resulting from interactions with the solvent. The net result for proteins is a hydrophobic polypeptide core protected from the solvent creating regions with a microscopic environment controlled and adapted for specific functions. In nucleic acids, tertiary structure is a result of an equilibrium between electrostatic forces due to the negatively charged phosphates, stacking interactions between the bases due partially to hydrophobic and dispersion forces, hydrogen bonding interactions between the polar substituents of the bases, and the conformational energy of the sugar–phosphate backbone. In its preferred conformations, the polynucleotide backbone exposes the negatively charged phosphates to the dielectric screening by the solvent and promotes the stacked helical arrangement of adjacent bases. In this way, a hydrophobic core is created where hydrogen bond formation between bases as well as additional sugar–base and sugar–sugar interactions are favored. In such helical structures, only the internal atoms involved in hydrogen bonding between the bases are protected from solvent with most of the other atoms accessible to water. Water can influence conformation because it is a highly polarizable dielectric medium, because it competes with intramolecular interactions like hydrogen bonding, and because it gives rise to hydrophobic interactions.