Correlation between antisense activity and RNA secondary structure

Li Liao1, Zhongwei Li2, University of Delaware;, Florida Atlantic University

Antisense oligonucleotides (AO) can specifically inactivate expression of a gene by binding to its mRNA. This regulatory effect of AO has been explored as potential therapeutic applications. It is therefore of great importance to understand what factors may affect the interaction of AO and the target RNAs. Previous studies suggested that activities of AO are affected by the local structure of the target RNA. In this work, we have conducted a statistical analysis on a set of 349 oligonucleotides whose activities of inactivating various mRNA targets were reported ( We analyzed the secondary structures of the target RNA sequences using the program RNAFold from Vienna RNA Package. AO and RNA targets are classified into five categories according to the predicted RNA local structural features at or close to the binding sites. Statistical analysis showed that the activities of AO are correlated with those local secondary structural features. High activity is more likely to occur at hairpin of multi-branched loops with flanking stems than at bulge loops or linear regions. Further analysis of sequences clearly representing various structural categories, and verification of the predictions by biochemical experiments will facilitate understanding of the interaction. The result will be useful for designing AO and other therapeutic RNA species.