Raman, polarized Raman and ultraviolet resonance Raman spectroscopy of nucleic acids and their complexes

Applications of Raman spectroscopy to investigate the molecular constituents of nucleic acids were initiated in the late 1960s and soon thereafter progressed to studies of synthetic and native nucleic acids and complex biological assemblies containing either DNA or RNA. Raman applications to nucleic acids have continued to increase in number and diversity up to the present time. This paper attempts to provide an overview of this large body of work, with emphasis on studies carried out during the past decade and focusing on problems of biological interest and significance. The specific Raman methodologies included in this review of nucleic acid applications are (i) conventional Raman spectroscopy (i.e. off-resonance Raman excitation), (ii) ultraviolet resonance Raman (UVRR) spectroscopy, and (iii) polarized Raman microspectroscopy. For each methodology, the experimentally obtained nucleic acid spectrum consists of a number of discrete vibrational bands, most of which can be assigned confidently to a base, sugar or phosphate constituent of the macromolecule and many of which can be employed as sensitive indicators or fingerprints of either local structure, global conformation, intermolecular interaction or molecular dynamics. The applications selected for review include numerous examples from the authors' laboratories. The topics addressed include the influences of base composition, base sequence, superhelical stress and drug ligation on nucleic acid structure and polymorphism, the thermodynamic parameters governing nucleic acid premelting and melting phenomena, the molecular mechanisms and determinants of protein/nucleic acid recognition and the structures and dynamics of nucleic acids in virus assemblies. Copyright (c) 2005 John Wiley & Sons, Ltd.