UV resonance Raman contribution to structure determination of the X form of double-stranded poly(dA-dT)

Abstract

Double-stranded poly(dA-dT) in aqueous solution and in the presence of a sufficient amount of a water soluble porphyrin (i.e. Cu(TMpy-P4)) can adopt a structure different from all canonical A-, B- and Z-DNA conformations. The corresponding circular dichroism (CD) spectra yield the same features as those of the so-called “X form” observed in highly concentrated CsF solutions of the same polymer. Resonance Raman spectra of this form were compared with those of the canonical B form of poly(dA-dT) obtained using the same UV excitation wavelengths (257 and 281 nm). No spectral modification of the adenine bands was observed which would imply any C2′-endo/anti to C3′-endo/anti or C3′-endo/syn sugar-pucker reorganization of the purine residues, as would be expected for the A or Z forms, respectively. Consequently, it is assumed that the conformation of adenine residues remains C2′-endo/anti, i.e characteristic of the B-DNA structure. In contrast, there is much spectral evidence that the sugar-puckering of thymine residues is different in the X form compared with that in the B form. Shifts and intensity changes in the ring and sugar coupled modes at 665, 745 and 784 cm −1 are interpreted in terms of a C3′-endo/anti reorganization of thymine residues. This B–X structural transition also induces modifications in the thymine C4O hydrogen-bond network with opposite adenine bases, as reflected in the variation in intensity of the 1370 cm −1 band and splitting of the 1660 cm −1 band.