AIM To optimize the antisense drug design based on the methods of secondary structure prediction of target mRNA by computer
and the quantitative
structure activity relationship analysis. METHODS The secondary structures of mRNA were predicted by the software RNAstructure, then the antisense
phosphorothioate oligodeoxynucleotides (AS ODN) were designed against the secondary structural elements. The in vitro anti tumor bioactivity of AS ODN was evaluated by A549 lung carcinoma cell line. The multiple regression was performed with the computer program SPSS. RESULTS AS ODN with high bioactivity concentrated on some local secondary structural motifs that were composed of several secondary structural elements, designated here as “target secondary structural motif” (target motif). The target motifs were relatively stable in the whole mRNA structures, but there were one or more unstable secondary structural elements (free energy>0) such as internal loops, knots, and hairpins, especially the bulge loops in the motif. Bioactivities of AS ODN targeting different “target motifs” were statistically different ( P <0 01) while AS ODN against the same “target motif” were with similar effects. CONCLUSION The concept of the “target motif” was helpful for optimizing the antisense drug design and might be useful for discovering the local function of mRNA and designing oligonucleotide probes and primers.