SELECTION OF ANTISENSE OLIGONUCLEOTIDES ON THE BASIS OF GENOMIC FREQUENCY OF THE TARGET SEQUENCE

Antisense oligonucleotides (ASOs) are capable of blocking the expressi on of targeted genes and are potential antitumor and antiviral therape utic agents. The specificity of ASO gene inhibition is compromised whe n homology to other sequences allows the selected ASO to bind to nonta rgeted mRNAs. To reduce this nonspecific activity, an ASO should targe t a sequence that is predicted to be unlikely to occur in other mRNAs. The probability of a sequence being unique can be predicted by determ ining the genomic frequency of short stretches of sequences contained within the target sequence. Two computer programs, OLIGOMER and HEXAGR APH, were developed for this analysis. OLIGOMER was used to analyze th e genomic frequencies of di-, tri-, and hexamers in more than 24 milli on nucleotides from 8 different genomes in GenBank. A mathematical mod el was developed that predicts the genomic frequency of longer oligome rs on the basis of the observed frequencies of shorter oligomers. The second program, HEXAGRAPH, was used to graphically display the genomic frequency data of a selected target gene. The computational tools dev eloped in this study may help to design more efficient ASOs by decreas ing their nonspecific binding activity.