How Flexible are DNA Constituents? The Quantum-Mechanical Study

Abstract

Relaxed force constants (RFCs) and vibrational root-mean-square deviations have been evaluated by the original calculation method for conformational parameters of the DNA structural units and their constituents: nucleic acid bases (uracile, thymine, cytosine, adenine and guanine) and their ‘building blocks’ (benzene, pyrimidine, imidazole and purine molecules), as well as the DNA backbone structural units: tetrahydrofuran, 1,2-dideoxyribose, methanol and orthophosphoric acid. It has been found that the RFCs for nomenclature torsions β, γ, ε and sugar pseudorotation angle P in 1,2-dideoxyribose are sensible to the molecule conformation and their values are in the range of 1–25 kcal/(mole-rad2) obeying the inequality K γ > K ε > KP > K β. The RFCs values for endocyclic torsions of nucleic acid bases six-member rings lie within 15–45 kcal/(mole·rad2) in pyrimidines and within 20–60 kcal/(mole·rad2) in purines. It is shown that the quantum zero-point motion effectively neglects the amino group non-planarity in cytosine, adenine and partially in guanine.