Introduction of 5′-Terminal Amino and Thiol Groups into Synthetic Oligonucleotides

Versatile 5'-functionalization of oligonucleotides on solid support: amines, azides, thiols, and thioethers via phosphorus chemistry

Although the preparation of conjugates of oligonucleotides is by now commonplace, existing methods (usually utilizing thiols or primary amines) are generally expensive, and often require postsynthetic reaction with the DNA followed by a separate purification. Here we describe simple procedures for a broad set of direct 5'-end (5'-terminal carbon) functionalizations of DNA oligonucleotides while they remain on the synthesizer column. 5'-Iodinated oligonucleotides (prepared by an automated cycle as previously reported) are converted directly to 5'-azides, 5'-thiocarbamates, and alkyl and aryl 5'-thioethers in high yields. Further, we demonstrate high-yielding conversions of DNA-azides to 5'-amines, and of thiocarbamates to 5'-thiols. Finally, we report a new, one-pot conversion of naturally substituted 5'-OH oligonucleotides (again on the solid support) to 5'-amino-oligonucleotides. All of the above reactions are demonstrated in multiple sequence contexts. Most of the procedures are automatable.

A 2'-O-thiol tether in the ribose moiety of nucleic acids for conjugation chemistry

A 2'-O-hexylthiotrityl adenosine phosphoramidite has been synthesized and incorporated into oligodeoxyribonucleotide (oligo) phosphodiesters and phosphorothioates. These oligos possess the lipophilic 2'-O-hexylthiotrityl group at pre-selected positions. Upon treatment with silver nitrate solution, a free thiol group was generated which was further functionalized. The new tether offers a convenient nucleophile for conjugation of various pendant moieties that would reside in the minor groove. Because of its versatility and location, the modification has a variety of potential applications, most notably as an enhancer of antisense activity.