Hydrogen bonds (H-bonds) are weak electrostatic interactions involving hydrogen atoms located between two atoms of higher electronegativity. Being weaker than covalent bonds, they are nevertheless the most significant interactions in the folding and stabilization of DNA and RNA molecules. H-bonds are directional due to the orbital shape of the electron density distributions, and thus favor planar base pair geometries formed by at least two H-bonds. Most one H-bond pairings are also planar due to stacking effects within the helical regions where they are found.
Base pairing between two nucleotides can be determined using the probabilistic method developed in our group, which yields a symbolic classification of the possible H-bonding patterns.
The classification is based on the involved faces of each base. Here, these faces are divided into many subfaces that better distinguishes between two pairing types. They were determined from a statistical and empirical analysis of observed base pairs and the details can be found in an article by Lemieux & Major.
In addition to the face oriented classification of base pairings, identification numbers are used in MC-Sym. Roman numerals indicate the two (or three) H-bonds pairings identified by Donohue [4,5] whereas arabic numerals indicate the bifurcated and single H-bond pairing patterns generated by Gautheret [8]. This nomenclature was introduced in pre-3.3 versions of MC-Sym and is preserved in newer version for backward compatibility. Table 3.2 summarizes the different parameters of base pair classification.