A proper understanding of the biological functions of nucleic acids requires a knowledge of the dynamic aspects of their structures. For example with DNA, first its structural elements which control replication, transcription, repair, condensation, packaging, and transport have to be elucidated. Then, the changes of such elements caused by the approach of other molecules and the relevant kinetics must be pursued. Because of the recent increase in the sensitivity of the Raman spectrometer, and the rapid evolution of detailed biochemical findings, Raman spectroscopy promises to play an important role in this field. The eight papers in this Special collection, illustrate the role of Raman spectroscopy.
Every Raman spectrum of a nucleic acid consists of more than 50 Raman bands in the 1800-100 cm 1 range. Our first task to establish an unequivocal assignment for each of these Raman bands. For such an assignment, a singlesite isotopic label of the molecule in question is extremely powerful, because the observed isotope frequency shift is known to be proportional to the square of the amount of displacement of the atom involved in the normal vibration in question. H. Takeuchi and his collaborators prepared seven isotopomers of guanosine, in each of which only one carbon, nitrogen, or oxygen atom was replaced by a stable isotope, 13 C, 15 N, or 18 O. With 257 nm excitation, they examined 16 Raman spectra of these eight guanosines in H 2 O and in D 2 O. They listed seven isotope shifts (namely, the displacements of 7 atoms in the molecule) for each of the 27 normal vibrations of guanosine and 28 normal vibrations of deuterated guanosine. All investigaton will benefit from this table, as far as they are dealing with the Raman spectrum of the guanosine portion of a nucleic acid.
An 'assignment' of a Raman band of a nucleic acid means, not only knowing the amounts of displacements of the atoms in the normal vibration in question, but also the molecular conformation in which the normal vibration in question takes place. Carmona and his collaborators showed that the uracil ring breathing vibration of uridine gives a strong Raman band at 780 cm 1 if the ribose has a C2 0 endo conformation, while it moves to 790 cm 1 if the ribose has a C3 0 endo conformation.
The double-helical DNA is converted partly into a single stranded form during its replication and transcription. Therefore, it is important to establish how the Raman signals are different in these two forms. This structural conversion also takes place when the DNA solution is heated to 70 Β°C or higher. G.J. Thomas et al. followed the changes in the Raman signals of calf thymus DNA caused by this structural conversion in detail (Biophysical Journal 69, 2623 (1995)). The Thomas group presents here the temperature dependence of the Raman bands of poly(dA-dT)Γpoly(dA-dT), which is a double-helical B DNA containing A.T and T.A base pairs in alternating sequence. The authors show Raman changes, not only for melting where the double-stranded structure dissociates, but also for premelting where the double-stranded structure is perturbed but does not dissociate (10-66 Β°C).
In connection with such a premelting of a double-helical nucleic acid, the finding of Barron et al. is striking. They measured Raman optical activity (ROA) of double-stranded poly(rA)Γpoly(rU) in the temperature range 2-45 Β°C, and plotted the intensities of three ROA couplets centred at 1252,