Computational methods for analysis of terahertz spectral signatures of nucleic acids

Motivated by the terahertz application to spectroscopic sensing of genetic and related materials, this paper focuses on the calculation of the absorption spectra of of poly(rG)-poly(rC) and poly(dA)-poly(dT) in the range 2-300 cm^-1. The potential energy of nucleic acids is minimized and the normal mode analysis is performed using AMBER 8 package. The calculated absorption spectra are compared to the previous modeling results using JUMNA & LIGAND package and to the experimental data. The position of the strongest RNA resonance peak from both programs agrees with that experimentally observed. The AMBER-based polarization results fit the experimental data reasonably well.