In this chapter the fundamental question of how does protein-DNA or protein-RNA interaction affect the structures and dynamics of DNA, RNA and protein is addressed. Models for calf-thymus DNA and transfer RNA interactions with human serum albumin (HSA), ribonuclease A (RNase A) and deoxyribonuclease I (DNase I) are presented here, using Fourier Transform Infrared (FTIR) spectroscopy in conjunction with UV-visible and CD spectroscopic methods. In the models considered, the binding sites, stability and structural aspects of protein-DNA and protein-RNA are discussed and the effects of protein interaction on the secondary structures of DNA and protein were determined.