Use of ribonucleosides as protecting groups in synthesis of polynucleotides with phosphorylated terminals

Two new protected 5'-ribonucleotides, 2'3'-O-bis(4,4'-dimethoxytrityl)uridine 5'-(4-chlorophenyl phosphate) and 2',3'-O-(methoxymethylene)uridine 5'-(4-chlorophenyl phosphate), form the basis of a chemical procedure for phosphorylating the 5'-ends of DNA fragments synthesized by the phosphotriester approach. Condensation of either of these mononucleotide units with the free 5'-hydroxyl of an otherwise fully protected oligomer results in high-yield formation of a 5'-5' triester linkage. Subsequently, the terminal ribonucleotide of the deprotected product rU5'-5'd(N-Nn-N) can be cleaved by periodate oxidation of its 2',3'-cis-hydroxyl system followed by beta-elimination, leaving its phosphate attached to the 5'-hydroxyl group of the oligodeoxyribonucleotide. This procedure together with a tactic employing a 2',3'-O-acylribonucleotide residue at the 3'-terminus of the chain allows the synthesis of oligomers possessing monophosphate groups at either end or both ends. Furthermore, oligonucleotide intermediates possessing a 5'-5'-linked uridine terminal are shown to have a special application as acceptors in RNA ligase reactions, where the presence of the ribonucleoside cap on the 5'-phosphate limits ligation specifically to the 3'-ends of the oligomers. Removal of the uridine residues to expose free 5'-phosphates would then enable the products to participate as donors in further elongation reactions.