S-N TRANSITION OF THE SUGAR RING IN B-FORM DNA

A conformational analysis method was applied to study the possible variations in deoxyribose geometry of B-form DNA duplexes. It is shown that in d(AAA).d(TTT) and d(GGG).d(CCC) trimers, extended on both sides by regular DNA helices, the conformation of a single sugar ring can deviate strongly from the standard C2'-endo. Pyrimidine deoxyriboses have significantly higher conformational freedom than purine deoxyriboses. The calculated conformer populations agree well with experimental data. The dependence of trimer energy on the pseudorotation angle P for the thymine deoxyribose has an additional local minimum in the Ol'-endo region (P = 85-degrees) with an energy only 0.5 kcal/mole higher than the energy of a main minimum (P = 140-degrees). Cytidine has several local minima in the N-region of conformations. A change in thymine sugar ring geometry of the AAA:TTT duplex creates a 5-degrees bend across the groove. The conformational mobility of deoxyriboses in free trimers was analyzed, as well as the spreading of structural perturbation to the neighboring nucleotides.