Local and overall conformations of DNA double helices with the A - T base pairs

Raman spectra have been observed of two different poly[d(A-T)].poly[d(A-T)] fibers, whose X-ray diffractions were confirmed to be purely of A and B forms. A number of spectral differences were found between the A and B forms of this DNA duplex, and they were ascribed to local conformational differences in the adenosine, thymidine and phosphodiester portions. The ascription was made on the basis of a separate series of Raman examinations on six crystals involving adenosine or thymidine, and fifteen other nucleotide crystals, whose structures are all known by previous crystallographic works. By taking these structure-spectrum correlations thus obtained into account, a Raman spectroscopic investigation was made of a few double-helical DNAs in aqueous solutions. It has been concluded that both poly[d(A-T)].poly[d(A-T)] and poly(dA).poly(dT) have a C2'endo-anti adenosine, C2'endo-anti thymidine, a b-type mainchain (beta = 160 +/- 15 degrees, gamma = 45 +/- 15 degrees, delta = 140 +/- 10 degrees) and an a2-type mainchain (beta = 210 +/- 10 degrees, gamma = 45 +/- 15 degrees, delta = 140 +/- 10 degrees) not only in low-salt medium but also in 6.6 M CsF solutions, where beta, gamma and delta are the torsion angles around O5'-C5', C5'-C4' and C4'-C3' axes, respectively. Poly(rA).poly(dT), on the other hand, was considered to have a heteronomous duplex structure, in which the poly(rA) strand has a C3'endo-anti adenosine and a1-type mainchain (beta = 175 +/- 25 degrees, gamma = 45 +/- 15 degrees, delta = 80 +/- 10 degrees) whereas the poly(dT) strand has a C2'endo-anti thymidine and b-type mainchain.