Understanding the underlying language code that governs the π–π non-covalent interactions between proteins and DNA

Protein–nucleic acid interactions are crucial for transferring biological information and rely on sequence-specific recognition. Here, we present our theoretical analysis of the parallel alignment of aromatic coupling between bases and the benzene rings found in three naturally occurring aromatic amino acids. Using a model of electron pairs in oscillatory resonant quantum states, the most stable geometry of the dimer involves positioning the benzene ring on one side of the base via parallel displacement. This occurs when the $${p}_{z}$$ orbitals of N3 and C2 in the purines interact with the C1 and C2 carbons of the benzene ring, and when the $${p}_{z}$$ orbitals of C5 and C6 in the pyrimidines interact with the C1 and C2 carbons of the aromatic benzene ring. The coupling Hamiltonian relates to a canonical transformation that preserves the system’s total energy. The dipole coupling can enhance quantum correlations. To estimate the interaction force, it is sufficient to adapt the Hellmann–Feynman theorem using the model of electron pairs in oscillatory resonant quantum states.