Cleaving Folded RNA by Multifunctional DNAzyme Nanomachines

• Published in: Chemistry : a European journal 2024-07, Vol.30 (40), p.e202401580-n/a
• Main Authors: Nedorezova, Daria D., Dubovichenko, Mikhail V., Eldeeb, Ahmed A., Nur, Moustapha A. Y., Bobkov, Gleb A., Ashmarova, Anna I., Kalnin, Arsenij J., Kolpashchikov, Dmitry M.
• Format: Article
• Language: English
• Subjects: Affinity; affinity/specificity dilemma; Binding; Deoxyribonucleic acid; Deoxyribozymes; DNA; DNA nanotechnology; DNA probes; DNAzyme; Gene silencing; Gene therapy; hybridization selectivity; mRNA; Nanotechnology; Nucleotide sequence; Oligonucleotides; Probes; Ribonucleic acid; RNA; RNA probes; RNA-mediated interference; Selectivity; Substrates
• ISSN: 0947-6539; 1521-3765; 1521-3765
• DOI: 10.1002/chem.202401580

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 for cleaving folded RNA by using multicomponent agents (dubbed ‘DNA nanomachine’ or DNM). DNMs bind RNA by four short RNA binding arms, which ensure tight and highly selective RNA binding. Along with the improved affinity, DNM maintain 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 derived by DNA nanotechnology in gene therapy. The developed multifunctional DNAzyme nanomachine (DNM) binds RNA by four short RNA binding arms, which ensure tight and highly selective RNA binding. The design can increase both the binding and product release steps of the DNAzyme catalytic cycle. The approach is efficient in cleaving RNA having stable secondary structures.