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.

Four benzophenanthridine phosphoramidite reagents have been prepared in which the linker chain between the benzophenanthridine and the phosphoramidite moiety is attached to C-2, C-6, C-9, and C-12 of the benzophenanthridine ring system. These benzophenanthridine phosphoramidites should prove to be useful in the syntheses of antisense oligonucleotide-intercalator conjugates in which the linker chain is attached to various regions of the benzophenanthridine intercalator. One of the new benzophenanthridine phosphoramidite reagents was used to prepare an antisense oligonucleotide-intercalator conjugate in which the oligonucleotide TCAGTGGTp was connected at its 5'-hydroxyl group through a linker chain to the C-2 hydroxyl group of a benzophenanthridine.

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