Backbone conformations in deoxyribonucleic acids. Conformational role of the 2′‐hydroxyl group on the internucleotide phosphodiester conformations

Abstract

AbstractThe conformations accessible to the internucleotide phosphodiester group in deoxydinucleoside monophosphates, deoxydinucleoside triphosphates, and deoxypolynucleotides have been explored in detail by potential energy calculations. The two most predominant conformations for the nucleotide moiety (3E and 2E) and their possible combinations (3E−3E, 3E−2E, 2E−2E, 2E−3E) have been employed, similar to our earlier studies on polyribonucleotides. The internucleotide P‐O bond torsions are very sensitive to the sugar pucker (3E and 2E) and sugar type (ribose and 2′‐deoxyribose) on the 3′‐residue of dinucleoside phosphates. The preferred phosphodiester conformations found for the deoxydinucleoside monophosphates and triphosphates, in general, follow the same pattern as those obtained for ribose sugars when the sugar on the 3′‐side of the molecule has the 3E sugar‐ring conformation. The internucleotide P‐O bonds show a greater degree of conformational freedom when the 3′‐sugar has the 2E pucker. The double gauche g−g− conformation for the phosphodiester, which leads to the overlap of the adjacent bases, is shown to be one of the energetically most favored conformations for all the sequence of sugar puckers. It is found that the 2E−2E sequence of sugar puckers shows a greater energetic preference for the stacked helical conformation (g−g−) than the (3E−3E) and the mixed sugar‐pucker combinations. This effect becomes more pronounced in going from a dinucleoside monophosphate to a dinucleoside triphosphate suggesting that the 2′‐deoxy sugars favor the 2E sugar pucker in di‐, oligo‐, and polydeoxyribonucleotide structures. In addition to g−g−, the conformations g+g−, tg−, g−t, tg+, and g+t are also found to be possible for the phosphodiester in a polydeoxyribonucleotide and their populations depend to some extent on the sugar‐pucker sequence. It is shown that the short‐range intramolecular interactions involving the sugar and the phosphate groups dictate to a large extent the backbone conformations of nucleic acids and polynucleotides.