Exclusion principle between the physicochemical properties of complementary nucleobases and symmetry breaking in double-stranded DNA conformations

Abstract

The information contained in DNA is encoded in a double helix formed by two antiparallel and complementary sequences of nucleotides, which are stabilized by hydrogen bonds. At physiological conditions, each nucleobase possesses three main characteristics; molecular structure, functional group, and orientation in the double helix. These properties produce steric constraints that allow only complementary interactions between nucleobase pairs to form double or triple hydrogen bonds. In this work, a mathematical model is proposed to describe the pairing interactions between nucleobases according to their physicochemical properties (structure, functional group and orientation). The results suggest that stable hydrogen bonds derived from nucleobase interactions can be represented by a set of 4 hermitian matrices and a Clifford Algebra Cl(4,0). Moreover, it is shown that the allowed interactions between pairs of nucleobases enable the formulation of an exclusion principle between the states of the observables. Finally, the mathematical representation of the hydrogen bonding between complementary nucleobases suggests a preferential orientation (chirality), which could be associated with the major groove in the double helix structure of B-DNA.