Conformational study of the trinucleoside tetraphosphate d(pCpGpCp)

Abstract

Conformational energy calculations have been carried out for the phosphodiester group and the sugar ring to find out the appropriate variable to represent the conformational change of polynucleotide chains. Energy map of dimethylphosphate anion, DMP$^-$, obtained by the analytical potential function shows a good agreement with the experimental data. Also, the local maximum of 4.5 kcal/mol at the (t,t) region is nearly the same as the value of 4.77 kcal/mol by the ab initio calculation. Energy variation along the pseudorotational paths of the sugar ring in $d(_pG_p)$ and $d(_pC_p)$ are plotted. The preference of purine sugar for the C2``-endo conformation satisfies the experimental data very well. The sugar ring without base has the energy barrier of 2.5 kcal/mol along the pseudorotational paths. Finally, topological transition of the handedness of the model compound, $d(_pC_pG_pC_p)$, is studied along the pseudorotational path of the sugar ring in guanosine. The left-handed form is about 41 kcal/mol higher in electrostatic energy than the right-handed form and this fact explains the former to be high salt form.