INVESTIGATIONS ON THE DYNAMIC STRUCTURES OF ADENINE-CONTAINING AND THYMINE-CONTAINING DNA

The structures of poly(dA-dT), poly(dA-dBr5U) and of poly(dA) · poly(dT) have been investigated in solution and in fibers, by Raman spectroscopy. Both the alternating poly(dA-dT), poly(dA-dBr5U) and non-alternating poly(dA) · poly(dT) exhibit, in the region of sugar phosphate backbone vibrations, two bands of almost equal intensity at about 841 cm-1 and 817 cm-1. The analysis of the characteristic bands of thymine residues that are sensitive to sugar puckers gives indication of a significant displacement from the C(2′)-endo conformer suggesting the adoption of alternative conformers such as O(4′)-endo. In contrast, the diagnostic Raman bands for the sugar pucker of adenine residues suggest, instead, predominant adoption of C(2′)-endo conformations. These Raman results are compatible with rapid dynamic changes of sugar puckers between C(2′)-endo and O(4′)-endo for the thymine (and uridine) residues, whereas in adenine residues the sugar puckers fluctuate around the C(2′)-endo pucker in all synthetic DNA molecules studied. Molecular dynamics simulations, performed on six different starting models using two distance-dependent dielectric functions ε(r) = 4r and a sigmoidal dependence), all gave similar dynamic behavior in agreement with these Raman data and their interpretation. The mean calculated pseudorotation phases of the adenine residues are systematically higher (around C(2′)-endo) than those of the thymine residues (close to O(4′)-endo-C(1′)-exo). Besides, the mean lifetimes of the thymine residues are 1.5 to 2.0-fold higher in the O(4′)-endo than in the C(2′)-endo domain, while those of the adenine residues are two to threefold higher in the C(2′)-endo than in the O(4′)-endo domain. In the Raman spectra of the alternating poly(dA-dBr5U), the splitting of a band into two components arising from the two contributions of ApBr5U and Br5UpA provides strong evidence for a repeating dinucleotide structure in solution. The calculated twist values averaged over the simulation runs are also systematically higher in the 5′T-A3′ step (39 °) than in the 5′A-T3′ step (33 °). Simultaneously, the calculated roll values are positive in the 5′T-A3′ step (6 °) and negative in the 5′A-T3′ step (-9 °), while the propeller twist values are about the same (-11 ° to -16 °). On the other hand, in the homopolymer, the average twist value is close to 36 ° with the roll angle close to 0 ° and large propeller twist values (-20 °). © 1992.