Temperature dependence of the raman spectrum of DNA. II. Raman signatures of premelting and melting transitions of poly(dA)·poly(dT) and comparison with poly(dA‐dT)·poly(dA‐dT)*

AbstractThe temperature dependence of the Raman spectrum of poly(dA)·poly(dT) (dA: deoxyadenosine; dT: thymidine), a model for DNA containing consecutive adenine·thymine (A·T) pairs, has been analyzed using a spectrometer of high spectral precision and sensitivity. Three temperature intervals are distinguished: (a) premelting (10 < t < 70°C), in which the native double helix is structurally altered but not dissociated into single strands; (b) melting (70 < t < 80°C), in which the duplex is dissociated into single strands; and (c) postmelting (80 < t°C), in which no significant structural change can be detected. The distinctive Raman difference signatures observed between 10 and 70°C and between 70 and 80°C are interpreted in terms of the structural changes specific to premelting and melting transitions, respectively. Premelting alters the low‐temperature conformation of the deoxyribose‐phosphate backbone and eliminates base hydrogen bonding that is distinct from canonical Watson–Crick hydrogen bonding; these premelting perturbations occur without disruption of base stacking. Conversely, melting eliminates canonical Watson–Crick pairing and base stacking. The results are compared with those reported previously on poly(dA‐dT)·poly(dA‐dT), the DNA structure consisting of alternating A·T and T·A pairs (L. Movileanu, J. M. Benevides, and G. J. Thomas, Jr. Journal of Raman Spectroscopy, 1999, Vol. 30, pp. 637–649). Poly(dA)·poly(dT) and poly(dA‐dT)·poly(dA‐dT) exhibit strikingly dissimilar temperature‐dependent Raman profiles prior to the onset of melting. However, the two duplexes exhibit very similar melting transitions, including the same Raman indicators of ruptured Watson–Crick pairing, base unstacking and collapse of backbone order. A detailed analysis of the data provides a comprehensive Raman assignment scheme for adenosine and thymidine residues of B‐DNA, delineates Raman markers diagnostic of consecutive A·T and alternating A·T/T·A tracts of DNA, and identifies the distinct Raman difference signatures for premelting and melting transitions in the two types of sequences. © 2002 John Wiley & Sons, Inc. Biopolymers 63: 181–194, 2002; DOI 10.1002/bip.10022