Abstract
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, RNA and protein were determined.
Highlights
Fourier Transform Infrared (FTIR) spectroscopy has widespread application to qualitative and quantitative analyses in chemistry, biochemistry, biology, medicinal chemistry and environmental science.H.A
DNA and RNA conformational transitions induced by ligand, drug or protein interactions were studied by FTIR spectroscopy
The DNA in-plane vibrations at 1750–1500 cm−1 related to the G–C and A–T base pairs and the back bone phosphate group at 1250–1000 cm−1 [42,43,49,50,51,52] were perturbed upon protein interaction
Summary
Fourier Transform Infrared (FTIR) spectroscopy has widespread application to qualitative and quantitative analyses in chemistry, biochemistry, biology, medicinal chemistry and environmental science. FTIR spectroscopy is an established method for the structural characterization of proteins, DNA and RNA. Changes in the secondary structure of proteins as a function of changes in pH, solvent composition, temperature, ligand binding, and exposure to DNA, RNA and lipids or other compounds in solution (e.g. drugs) have been investigated. DNA and RNA conformational transitions induced by ligand, drug or protein interactions were studied by FTIR spectroscopy. The biological significance of protein complexation with RNA has been well recognized, the specific mechanism of protein–RNA interaction is not fully understood [10]. Structural analysis of calf-thymus DNA and transfer RNA interactions with HSA, RNase A and DNase I are presented here, using Fourier Transform Infrared (FTIR) in conjunction with UV-visible and CD spectroscopic methods. The binding sites, stability and structural aspects of protein–DNA and protein–RNA complexes are discussed and the effects of protein interaction on the secondary structures of polynucleotides and protein are reported here
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