Towards rational design of antisense DNA: molecular modelling of phosphorothioate DNA analogues

In order to assess the effects of substitution of one of the non-bridging oxygens in the phosphodiester group with sulfur, molecular dynamics calculations were performed on duplex oligodeoxynucleotides having a complete helical turn, [d(CpGpCpGpApApTpTpCpGpCpG)]2. The calculations were carried out with the unmodified duplex, as well as with duplexes having one phosphorothioate strand with uniform phosphorus stereochemistry (SP or RP). The electrostatic and structural (equilibrium molecular dimensions as well as force constants) parameters of the phosphorothioate group for molecular mechanics and dynamics calculations were derived from ab initio quantum mechanics optimizations of conformers of O,O'-dimethyl phosphorothioate. Molecular dynamics simulations (30 ps) were carried out using the AMBER force field, with explicit inclusion of all hydrogen atoms, counterions, and water. The simulations indicate a significant decrease of stability of the model containing the homochiral RP-phosphorothioate strand, whereas the model containing the homochiral SP-phosphorothioate strand has practically the same energy as the unmodified oligodeoxynucleotide duplex. The energy difference determined indicates some preference for the use of stereochemically pure SP-phosphorothioates as antisense gene inhibitors. Moreover, the significance of these results in connection with use of phosphorodithioates is discussed.