Conformational Properties of the Deoxyribose and Ribose Moieties of Nucleic Acids:  A Quantum Mechanical Study

The present work analyzes the intrinsic conformational energetics associated with the puckering of the deoxyribose and ribose sugars in nucleic acids using high-level ab initio quantum mechanical calculations. A variety of model compounds have been designed to define the minimal structural unit suitable to model the sugar moiety in nucleic acids. Results suggest that all the structural features of a nucleoside are required to model the sugar moiety of nucleic acids. Stuctures calculated at the MP2 level of theory are in close agreement with experimental structural information. In deoxyribose, the south pucker (B form of double helices) is intrinsically favored over the north pucker (A form of double helices) by ∼1.0 kcal/mol. In contrast, for ribose, with torsion ε in an RNA-like conformation, the north pucker is favored over the south pucker by ∼2.0 kcal/mol. For both the deoxyribose and ribose of nucleic acids, the lowest energy barrier between the north and south puckers is >4.0 kcal/mol. The present calculations suggest that crossing this barrier may involve a decrease in the amplitude of the furanose ring. Implications of these results with respect to nucleic acid stucture and dynamics are discussed.