Cleaving Folded RNA by Multifunctional DNAzyme Nanomachines

Abstract

Both tight and specific binding of folded biological mRNA is required for gene silencing by oligonucleotide gene therapy agents. However, this is fundamentally impossible using the conventional oligonucleotide probes according to the affinity/specificity dilemma. This study addresses this problem by using multicomponent agents (dubbed ‘DNA nanomachine’ or DNM) for RNA binding. DNMs bind RNA by four short RNA binding arms, which ensures tight and highly selective RNA binding. Along with the improved affinity, DNM maintained the high sequence selectivity of the conventional DNAzymes. DNM enabled up to 3‐fold improvement in DNAzymes catalytic efficiency (kcat/Km) by facilitating both RNA substrate binding and product release steps of the catalytic cycle. This study demonstrates that multicomponent probes organized in sophisticated structures can help to achieve the balance between affinity and selectivity in recognizing folded RNA and thus creates a foundation for applying complex DNA nanostructures in gene therapy.