[Comparative conformational analysis of dinucleoside phosphate CpA and its analog C(3'NH)pA]

By the method of theoretical conformational analysis, on the examples of CpA and C(3'NH)pA comparison is made of conformational flexibility of dinucleoside phosphates with the natural O-P-O and abnormal N-P-O internucleotide bonds. The conformational flexibility of sugar cycles is accounted for. It is shown that substitution of the phosphodiester bond into amide ester leads to a noticeable limitation of favorable areas in conformational space of molecules and, as consequence, to the increase of the equilibrium ratio of conformers with the Pba and Mbb type of base stacking. The obtained results are used for discussion of the binding experiments of acylamino acid derivatives of CpA and C(3'NH)pA to the donor site of the peptidyl transferase center of ribosomes.