[Study of the relationship between secondary DNA strucure and base sequence by the technic of theoretical...

An investigation of double-stranded polynucleotide conformations using the algorithm for exclusion of redundant dihedral angles and flexible sugar unit has been performed. The fragment of DNA including three nucleotide pairs was taken into account for polynucleotides poly[d(A--T)].poly[d(T--A)], poly[d(G--C)].poly[d(C--G)], poly(dA).poly(dT) and poly(dG).poly(dC). The resulting structures being energetically optimal have helical parameters corresponding to X-ray experimental values for A- and B-forms. It was revealed that B-form is the most energetically favorable structure, therefore the earlier conception that water is of importance for B-form stabilisation may be revised. Relative stabilities of B- and A-forms depend upon base sequence because unequal contributions of the stacking and backbone energy in whole potential energy of the structrues with different sequences.