CONFORMATIONAL PROPERTIES OF THE DEOXYRIBOSE AND RIBOSE MOIETIES OF NUCLEIC-ACIDS - A QUANTUM-MECHANICAL STUDY

The present work analyzes the intrinsic conformational energetics asso ciated with the puckering of the deoxyribose and ribose sugars in nucl eic 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. R esults suggest that all the structural features of a nucleoside are re quired to model the sugar moiety of nucleic acids. Stuctures calculate d at the MP2 level of theory are in close agreement with experimental structural information. In deoxyribose, the south pucker (B form of do uble helices) is intrinsically favored over the north pucker (A form o f double helices) by similar to 1.0 kcal/mol. In contrast, for ribose, with torsion epsilon in an RNA-like conformation, the north pucker is favored over the south pucker by similar to 2.0 kcal/mol. For both th e deoxyribose and ribose of nucleic acids, the lowest energy barrier b etween the north and south puckers is >4.0 kcal/mol. The present calcu lations suggest that crossing this barrier may involve a decrease in t he amplitude of the furanose ring. Implications of these results with respect to nucleic acid stucture and dynamics are discussed.