Sequence-Programmable DNA Capsules with RNA-Responsive Cargo Release and Gene Regulation

Abstract Intracellular RNA regulates diverse cellular processes and represents an attractive target for materials-based control of gene expression. Here, we report a sequence-engineered DNA capsule platform that couples RNA recognition to programmable cargo release. The capsules are assembled via layer-by-layer hybridization of designed DNA strands onto calcium carbonate (CaCO3) templates, forming a hollow DNA shell in which antisense oligonucleotides (ASOs) function as both regulatory modules and molecular triggers. Upon hybridization with complementary target sequences, toehold-mediated strand displacement (TMSD) converts sequence recognition into controlled payload release while concurrently modulating transcript levels. Two capsule variants targeting MYH9 and p21 were constructed as model systems. Using DNA analog target sequences, the capsules showed concentration-dependent and sequence-selective responses with limits of detection of 16.7 nM and 7.9 nM for MYH9 and p21, respectively. Importantly, MYH9 RNA also triggered concentration-dependent tetramethylrhodamine-dextran (TMR-D) release, with a limit of detection of 14.0 nM, supporting the RNA-responsive nature of the capsule design. Cell-based experiments showed cell-associated fluorescence signals and sequence-dependent changes in migration and viability. Co-encapsulation of doxorubicin-modified dextran (DOX-D) further reduced cell viability relative to unloaded capsules. These results demonstrate a proof-of-concept nucleic acid material in which sequence-level design governs stability, RNA responsiveness, and triggered release behavior. This DNA capsule platform provides a modular framework for RNA-responsive biomaterial design and for integrating sensing and functional outputs at the cellular level.