SELECTING EFFECTIVE ANTISENSE REAGENTS ON COMBINATORIAL OLIGONUCLEOTIDE ARRAYS

An array of 1,938 oligodeoxynucleotides (ONs) ranging in length from m onomers to 17-mers was fabricated on the surface of a glass plate and used to measure the potential of oligonucleotide for heteroduplex form ation with rabbit beta-globin mRNA. The oligonucleotides were compleme ntary to the first 122 bases of mRNA comprising the 5' UTR and bases 1 to 69 of the first exon. Surprisingly few oligonucleotides gave signi ficant heteroduplex yield. Antisense activity, measured in a RNase H a ssay and by in vitro translation, correlated well with yield of hetero duplex on the array. These results help to explain the variable succes s that is commonly experienced in the choice of antisense oligonucleot ides. For the optimal ON, the concentration required to inhibit transl ation by 50% was found to be five times less than for any other ON. We find no obvious features in the mRNA sequence or the predicted second ary structure that can explain the variation in heteroduplex yield. Ho wever, the arrays provide a simple empirical method of selecting effec tive antisense oligonucleotides for any RNA target of known sequence.