Fundamental differences in the equilibrium considerations for siRNA and antisense oligodeoxynucleotide design.

ABSTRACT: Both siRNA and antisense oligodeoxynucleotides (ODNs) inhibit the expression of a complementary gene. In this study, fundamental differences in the considerations for RNA interference and antisense ODNs are reported. In siRNA and antisense ODN databases, positive correlations are observed between the cost to open the mRNA target self-structure and the stability of the duplex to be formed, meaning the sites along the mRNA target with highest potential to form strong duplexes with antisense strands also have the greatest tendency to be involved in pre-existing structure. Efficient siRNA have less stable siRNA-target duplex stability than inefficient siRNA, but the opposite is true for antisense ODNs. It is, therefore, more difficult to avoid target self-structure in antisense ODN design. Sel

SUBMITTER: Lu ZJ 

PROVIDER: S-EPMC2441788 | biostudies-literature | 2008 Jun

REPOSITORIES: biostudies-literature