Investigations on the dynamic structures of adenine- and thymine-containing DNA

Abstract

The structures of poly(dA-dT), poly(dA-dBr 5U) 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-dBr 5U) 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) = 4 r 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-dBr 5U), the splitting of a band into two components arising from the two contributions of ApBr 5U and Br 5UpA 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 °).