RNA mapping: selection of potent oligonucleotide sequences for antisense experiments

The importance of finding good antisense sequences cannot be underestimated. Poor inhibition of the targeted protein can compromise the final outcome of an antisense experiment, making it difficult to arrive at a definitive understanding of the function of the protein of interest. In antisense therapeutics, identification of potent sequences becomes even more important. RNA mapping greatly increases the odds of finding active sequences. When antisense sequences are selected randomly or by gene walking, a substantial number of the oligonucleotides have little to no activity. In contrast, oligonucleotides selected by RNA mapping typically produce an antisense inhibition of greater than 50%. Oligonucleotides targeted to 60% of the accessible sites in the 5' portion of the multidrug resistance transcript inhibited P-glycoprotein function with high potency. In the angiotensin type 1 receptor system, oligonucleotides to the eight accessible sites examined inhibited AT1 receptor binding by at least 50%, with oligonucleotides to four of the sites producing at least 70% inhibition. The RNA mapping assay, which is based on standard molecular techniques, therefore provides an easy and reliable method for potent antisense sequence selection.