Structure and stability of the consecutive stereoregulated chiral phosphorothioate DNA duplex

The duplex structures of the stereoregulated phosphorothioate DNAs, [R-p,R- p]- and [S-p,S-p]-[d(GC(ps)T(ps)ACG)] (ps, phosphorothioate; PS-DNA), with their complementary RNA have been investigated by combined use of H-1 NMR a nd restrained molecular dynamics calculation. Compared to those obtained fo r the unmodified duplex structures (PO-DNA.RNA), the NOE cross-peak intensi ties are virtually identical for the PS-DNA.RNA hybrid duplexes. The struct ural analysis on the basis of the NOE restraints reveals that all of the th ree DNA.RNA duplexes take a A-form conformation and that there is no signif icant difference in the base stacking for the DNA.RNA hybrid duplexes, On t he other hand, the NOE cross-peak intensities of the protons around the cen tral T(ps)A step of the PS-DNA DNA duplexes are apparently different from t hose of PO-DNA.DNA. The chemical shifts of H8/6 and H1' at the T(ps)A step are also largely different among PS-DNA.DNAs and PO-DNA.DNA, suggesting tha t the DNA.DNB structure is readily changed by the introduction of the phosp horothioate groups to the central T(p)A step. The structure calculations in dicate that all of these DNA DNA duplexes are B-form although there exist s ome small differences in helical parameters between the [R-p,R-p]- and [S-p ,S-p]PS-DNA.DNA duplexes. The melting temperatures (T-m) were determined fo r all of the duplexes by plotting the chemical shift change of isolated pea ks as a function of temperature. For the PS-DNA.RNA hybrid duplexes, the [S -p,S-p] isomer is less stable than the [R-p,R-p] isomer while this trend is reversed for the PS-DNA.DNB duplexes. Consequently, although the PS-DNA.RN A duplexes take the similar A-form structure, the duplex stability is diffe rent between PS-DNA.RNA duplexes. The stability of the DNA.RNA duplexes may not be governed by the A-form structure itself but by some other factors s uch as the hydration around the phosphorothioate backbone, although the T-m difference of the DNA.DNA duplexes could be explained by the structural fa ctor.