Nano-sized cubes made from nucleic acid material (NANPs) are ideal scaffolds for therapeutic nucleic acids (TNAs). Both utilize sequence specificity through base-pairing, providing controlled strand interaction, stability, and targeted targeting delivery. However, there is a lack of research concerning nucleic acid compositions as therapeutic carrier agents and cytokine production. Exogenous NANPs and TNAs are subject to detection by immune cell receptors that can initiate undesired immune responses, threatening therapeutic reliability. The present research explores interferon-beta and interleukin-6 production induced by NANPs in human microglial cells based on nucleic acid composition and provides insight into hybrid NANPs as therapeutic drug carriers. IL-6 and IFN-β capture-specific ELISAs were used to assess immune response protein levels when cells were exposed to a 64-hybrid cube panel of 3-dimensional, six-stranded NANPs. Select hybrid NANP cubes with three RNA strands provoked significant IL-6 levels compared to carrier alone, and IFN-β production was significant for cubes NANPs with more than two RNA strands. Surprisingly, our results indicated only moderate cytokine production with increased RNA strands, an effect that was not statistically significant.