Backbone conformations in secondary and tertiary structural units of nucleic acids. Constraint in the phosphodiester...

The possible backbone phosphodiester conformations in a dinucleoside monophosphate and a dinucleoside triphosphate have been investigated by semiempirical energy calculations. Conformational energies have been computed as a function of the rotations omega' and omega about the internucleotide P-O(3') and P-O(5') linkages, with the nucleotide residues themselves assumed to be in one of the preferred [C(3')-endo] conformations. The terminal phosphates in a dinucleoside triphosphate greatly limit the possible conformations for the backbone (in a polynucleotide) compared to a dinucleoside monophosphate. There appear to be two major types of conformations that are favored for the backbone. The phosphodiester conformation (omega',omega) approximately (290 degrees ,290 degrees ) characteristic of helical structures is one of them, indicating that the polynucleotide backbone shows an inherent tendency for the helical conformation. The other favored conformation is centered at (omega',omega) approximately (190 degrees ,300 degrees ) and results in an extended backbone structure with unstacked bases. A third possible conformation centered at (omega', omega) approximately (200 degrees , 60 degrees ) and the (190 degrees , 300 degrees ) conformation appear to be important for the folding of a polynucleotide chain. The conformation (omega',omega) approximately (80 degrees ,80 degrees ), observed in a dinucleoside monophosphate and believed to be a candidate for producing an abrupt turn in a polynucleotide chain, is found to be stereochemically unfavorable in a dinucleoside triphosphate and a polynucleotide.