Structure of DNA predicted from stereochemistry of nucleoside derivatives

Abstract

CRYSTALLOGRAPHIC data on the constituents of nucleic acids can be very useful in predicting secondary structures. Until recently only data from the crystal structures of mononucleosides and mononucleotides have been used in building models of secondary structures for nucleic acids and polynucleotides. However, such data only provide information about the stereochemistry of nucleotides and not the relative orientation of the nucleotides around the 3′ and 5′ phosphodiester bonds. This relative orientation is the key factor which determines the secondary structure of nucleic acids and details of this orientation can be obtained from single-crystal study of dinucleoside monophosphates and other higher oligomers. So far, crystal structure data on the dinucleoside monophosphates GpC (sodium salt)¹, GpC (calcium salt)², ApU³, UpA⁴, a dinucleotide pTpT⁵, a trinucleoside diphosphate ApApA⁶, and a tetranucleotide pApTpApT (M.A. Viswamitra, personal communication) are available. We have analysed the conformations of these molecules and present here stereochemical criteria for the backbone of the poly-nucleotide chains and the nucleic acids. Application of these criteria to nucleic acids indicates type II structure for DNA, as proposed previously by us⁷ as an alternative to the double helix.