Temperature dependence of the Raman spectrum of DNA. Part I - Raman signatures of premelting and melting transitions of poly(dA-dT)center dot poly(dA-dT)

Poly(dA-dT) poly(dA-dT) is a double-helical B DNA containing A . T and T . A base pairs in alternating sequence; Although Raman spectra of this struct ure have been reported previously, the temperature dependence of the Raman bands has not been examined in detail. Using a spectrometer of high spectra l precision and sensitivity, we applied Raman difference spectroscopy to de termine the temperature dependence of all Raman bands of poly(dA-dT) poly(d A-dT) in physiological salt solutions (both H2O and D2O) over the temperatu re range 10-85 degrees C, Three temperature domains are distinguished by Ra man spectroscopy: premelting (10 < t < 66 degrees C), in which the double-s tranded structure is perturbed but does not dissociate; melting (66 < t < 7 5 degrees C), in which the double-stranded structure dissociates; and postm elting (75 < t < 85 degrees C), in which no structural change can be detect ed, The results demonstrate that distinct Raman difference signatures exist for the premelting and melting transitions, and that each involves changes in most Raman bands, Among other novel findings and assignments: (i) Raman bands at 728 (dA), 1236 (dT) and 1301 cm(-1) (dA) provide the most sensiti ve measures of base stacking in both the premelting and melting domains. (i i) Raman bands at 1182 (dT) and 1512 cm(-1) (dA) provide the most sensitive measure of T unpairing in the melting domain, An unexpected finding is the apparent correlation of the 1182 cm(-1) band intensity with the degree of thymine unpairing, Additionally, bands at 1376 (dT) and 1577 cm(-1) (dA) co nfirm changes in interbase hydrogen bonding with premelting, (iii) The temp erature dependence of the Raman band at 819 cm(-1) is closely correlated wi th those of backbone marker bands at 792 and 842 cm(-1) (O-P-O stretch mode s), indicating that the 819 cm(-1) band is due to a vibrational mode locali zed in the backbone and is diagnostic of phosphodiester torsions alpha/xi a pparently specific to the gauche-/trans conformation of B-II DNA, (iv) The Raman band at 1484 cm(-1) (dA) is sensitive to hydrogen bonding at the aden ine N1 site, (v) Comparison of spectra from H2O and D2O solutions reveal si gnificant vibrational coupling between Raman bands of the deoxynucleoside r esidues and B-form backbone of poly(dA-dT) poly(dA-dT). These results const itute an important foundation for future Raman studies of premelting and me lting phenomena in other DNA sequences, including poly(dA) poly(dT). Copyri ght (C) 1999 John Wiley & Sons, Ltd.