Conceptual simplicity, the possibility of rational design, relatively inexpensive cost, and developments in the sequencing of human genome have led to the use of short fragments of nucleic acid, commonly called oligonucleotides, either as therapeutic agents or as tools to study gene function. Furthermore, in the past decade, the development of antisense oligonucleotide technologies as therapeutics agents has led to Food and Drug Administration approval for the commercialization of the first antisense oligonucleotide, Vitravene (for cytomegalovirus retinitis; Refs. 1 and 2), and to numerous clinical trials of therapeutic oligonucleotides (3). The concept underlying antisense technology is relatively straightforward: the use of a sequence, complementary by virtue of Watson-Crick bp hybridization, to a specific mRNA can inhibit its expression and then induce a blockade in the transfer of genetic information from DNA to protein. However, although antisense oligonucleotides are commonly in use now both in the laboratory and clinic, this theoretical simplicity belies the many questions concerning the molecular mechanisms of action of these compounds. It is our contention that a highly critical approach must still be taken in interpreting data derived from experiments using antisense oligonucleotides. It remains relatively easy to claim that experimentally observed biological effects occur by an antisense mechanism; nevertheless, it is also easy to ignore those nonspecific effects that can provide a virtually identical explanation of the observed phenotype, especially when oligonucleotides with phosphorothioate backbones are used. These themes will be expounded in some detail in this review.
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