Oligonucleotide analogues: an overview

The medicinal chemistry effort directed toward improving antisense and antigene oligonucleotides has synthesized a large number of phosphate, ribose and heterocyclic base analogues. The phosphorothioate linkage is currently still the analogue linkage of choice for antisense studies. This is despite many years of effort to find alternatives that overcome the limitations of phosphorothioates. A number of modifications to phosphate and ribose have resulted in enhanced binding to RNA as measured by Tm, but generally the biological effects have been less dramatic. Currently, the most potent oligonucleotides have capitalized on recruiting the cellular enzyme RNase H to perform sequence-specific destruction of a targeted RNA. Virtually all modifications to phosphate or ribose other than phosphorothioate result in the loss of this recruitment. Chimeric strategies have overcome this limitation. Affinity and potency can additionally be improved by modifying the Watson-Crick-pairing heterocycles. Recent years have brought much consensus in terms of the mechanism of action of antisense oligonucleotides. A controversial area is the ability of oligonucleotides to permeate cells in whole animals. This issue will determine if antisense and triple helix technology results in practical broad-based therapeutics.