Advances in nanotechnology have resulted in the introduction of new materials for therapeutic and diagnostic purposes. In particular, DNA and RNA are viewed as representative and generic nano-blocks because of their physiochemical characteristics of specificity and nanoscopic-level accuracy. In addition, the intrinsic biocompatibility of DNA and RNA and their immune stimulation effects make these molecules ideal candidates for the rational design of novel bio-drug molecules. Recently, we reported novel RNA-DNA hybrid stem-loop structures that target and are endocytosed by LNCaP prostate cancer cells with high specificity. To effectively ligate the DNA and RNA modules in this research, we thoroughly evaluated and optimized several ligation parameters, and observed that we could enhance the ligation efficacy by changing the overhang sequences. A change in sequence information (GCAT) resulted in a 4-fold increase in ligation efficiency in comparison with other ligation factors. To determine the in vitro cellular targeting ability of the nanostructures, RNA-DNA hybrid constructs were complexed with gold nanorods (AuNRs), and the ability of these nanorods to target prostate cancer cells was highest at a 2 : 10 molar ratio of LNCaP cancer-specific looped A10 RNA to stem-DNA. Furthermore, doxorubicin (Dox) as a representative anti-prostate cancer therapeutic was loaded into the DNA-RNA hybrid nanostructures. Our results indicate that RNA-DNA hybrid constructs are effective anti-prostate cancer drug delivery platforms and can be employed for both discovery and delivery.