B cells are a crucial component of the immune system that respond to pathogens such as viruses through antibody production. Efficient activation of these cells is a primary goal in the design of next-generation vaccines. In this study, the application of DNA origami and peptide nucleic acid (PNA) nanostructures in vaccine design was investigated. The main objective was to assess the stability and potential of these architectures for multivalent antigen presentation aimed at effective B-cell activation. To this end, molecular dynamics simulations were employed to analyze the stability and dynamic behavior of DNA origami structures and virus-like particles under different temperature conditions. The results demonstrated that these structures maintained their integrity across a range of temperatures, indicating that thermal variations had no adverse effect on their architecture. Furthermore, the findings revealed that the dissociation force of DNA from PNA remained largely unaffected by temperature changes. Collectively, these results suggest that DNA origami and PNA nanostructures can remain stable under diverse environmental conditions, and the insights gained from this study may contribute to the design of stable and effective vaccines, as well as to the development of genetic therapies.