Identification of a SARS-CoV-2 Spike RNA-Cleaving DNAzyme and Optimization of Its AS1411 Chimera

Sequence-specific cleavage of viral RNA by deoxyribozymes offers a direct approach for suppressing viral gene expression, although limited cellular accessibility remains a major barrier to their functional application. In this study, a panel of eight deoxyribozymes representing different catalytic motifs and target regions was designed against SARS-CoV-2 Spike RNA and comparatively evaluated through time-dependent in vitro cleavage assays. Substantial target-site-dependent differences were observed even among candidates sharing the same catalytic core, demonstrating that catalytic performance was strongly influenced by the selected RNA target region. Among the tested sequences, 8-17-769 exhibited the fastest and most reproducible cleavage profile and the highest observed rate constants, and was therefore selected as the catalytic module for subsequent chimera development. To evaluate its activity in a cellular context, 8-17-769 was combined with the nucleolin-binding aptamer AS1411 in two opposite linear orientations. In an A549-based Spike expression model, both AS1411-containing chimeras were associated with reduced S gene expression, with 8-17-769-AS1411 producing the strongest response, corresponding to an approximately tenfold reduction relative to the reference group and reaching statistical significance (p < 0.05). The functional difference between the two orientations was further examined structurally. Circular dichroism spectroscopy showed that 8-17-769-AS1411 more closely preserved the spectral characteristics of the individual components, while computational analyses indicated a dynamic organization more similar to the free deoxyribozyme-RNA complex and a nucleolin-compatible docking configuration. Collectively, these findings identify 8-17-769 as a lead Spike RNA-cleaving deoxyribozyme and demonstrate that the linear organization of aptamer and catalytic modules can substantially influence the structural and functional properties of aptamer-deoxyribozyme chimeras.