Forces Stabilizing Associations Between Bases: Hydrogen Bonding and Base Stacking

Before describing structural features of nucleotides and their oligo- and polymeric complexes, a few remarks about base-base interactions are in order. These interactions are of two kinds: (a) those in the plane of the bases (horizontal) due to hydrogen bonding and (b) those perpendicular to the base planes (base stacking) stabilized mainly by London dispersion forces and hydrophobic effects. Hydrogen bonding is most pronounced in nonpolar solvents where base stacking is negligible, and base stacking dominates in water where base-base hydrogen bonding is greatly suppressed due to competition of binding sites by water molecules. Both are individually accessible to measurement and have been investigated in detail, especially hydrogen bonding because it is fundamental to the genetic code. For reviews see Refs. (448,449).