Vibration spectra of DNA and RNA segments

Abstract

The dispersion curves and density of states are used to analyze the vibrational characteristics of DNA and RNA segments. This is done using a harmonic Hamiltonian and the Green’s function technique. Two configurations of DNA and RNA, finite and cyclic, have been investigated and compared to their infinite counterparts. For the DNA molecule, three models, including a fishbone model, a ldder model, and a fishbone ladder model, have been employed, while the RNA molecule has been represented using a half fishbone model. To enhance the realism of DNA and RNA simulations, the unit cells within each infinite system as well as the length of the finite and cyclic cases are gradually enlarged. The connections between the sub-sites have been modeled using linear springs, where the stiffness of the vertical springs exhibits random variations throughout the length of the DNA and RNA models. Shorter DNA and RNA segments exhibit additional peaks in their density of states, resulting in more bands in dispersion curves. This indicates that as the number of building blocks grows in these segments, their curves resemble those of infinite systems. These findings have practical implications for studying the vibration characteristics of similar macro-systems.